Matrix: Virus
by wh1te rabb1t 01
Summary: It was all a lie, another system of control. But, inevitably, every lie comes crashing down on its creators.
1. Prologue: The Dream

**

Matrix: Virus

**

_"Tomorrow we could all be dead. But how would that be different from any other day? This is a war. We are soldiers. Death could come for us at any time. Now consider the alternative. What if I am right? Then tomorrow the war could be over. Isn't that worth fighting for? Isn't that worth dieing for?"_****

* * *

**Prologue: The Dream**

_Neo's feet pounded on the floor as he raced along the corridor. He grabbed the handle of a door and pulled back, flinging it open and dashing inside. He ran past a frozen security guard and through another door. Neo turned his head and glanced behind him._

_ Smith was close on his heels. Neo fired over his shoulder twice and Smith stopped to dodge. The bullets struck the pipe behind Smith's head. Neo dashed ahead and leapt over a pipe in his path. Turning left, he entered a tunnel made up of pipes. A bullet hit the pipe to one inch the left of Neo's head. Gas spurted out of the ruptured pipe and quickly spread throughout the area. Neo's phone rang._

_ "Neo, that's explosive gas! Whatever you do, don't fire any weapons!'_

_ "Great, thanks Voyd."_

_ Neo hung up and continued running. He came to a door and opened it. A man stepped out. Neo gasped._

_ "It was you all along!"_

_ "That's right," the man answered. "Me."_

_ "But why?"_

_ "Because I am sick of this pointless fighting, Neo. You know Neo. I know what he told you. There's no hope. So the machines will hook me up, plug me in. In exchange for your code."_

_ "Traitor!"_

_ "Exactly. Now, this might hurt a little."_

_ The man squared of and sent a kick flying at Neo's head. Neo grabbed his foot and twisted it, but the man brought his other leg around, smashing Neo in the face. Neo staggered backwards, and the man flipped around in the air, landing on his feet. Neo recovered and rushed to meet him._

_ The man punched at Neo, who grabbed his fist and flipped over him, kicking the man in the back. The man went flying into a wall. He picked himself off the floor and drew his gun._

_ "I tire of this game." He fired._

_ Neo stared in shock at the bullet in his left shoulder. _

_ "What the hell?"_

_ The man smirked triumphantly. _

_ "Your powers won't work here, Neo."_

_ He pointed the pistol at Neo's head and pulled the trigger-_

-Trinity woke up with a gasp. She glanced around the cabin, and saw to her surprise that Neo was gone. She got up and walked out of the room they shared. She slowly made her way to the galley. She dragged a chair out from under the table and plopped down in it, grabbing a cup of hot coffee from the counter as she did.

"Couldn't sleep?" a voice asked, startling Trinity. She glanced up to see Rabbit, one of the newer crew members. Rabbit was a hacker, completely and wholly dedicated to changing the system from the inside. He was one of the best hackers Trinity had ever seen. _But, _ Trinity thought with a slight smile, _not as good as me._

He had a quiet, introspective personality that put those around him at ease. He was kind, thoughtful, and intelligent. He had light sandy-brown hair and was shorter than average. His eyes were bright green. He had been Trinity's best friend inside the Matrix, and his search for her after she was unplugged led him to the Truth.

"No," she answered, smiling as old memories came back. Rabbit had asked her the same question the night before she was unplugged. She had told him goodbye and walked to the Adams Street Bridge, thinking she'd never see him again. Fortunately, she was wrong.

"Why not?" Rabbit inquired.

"Nothing, just a bad dream."

Rabbit pulled up a chair across from her and sat down, staring into her eyes. 

"_Just _a bad dream? You don't look like you had _just _a bad dream. Why don't you tell me about it?"

Trinity took a sip of her coffee. 

"It was nothing. I just saw…"

"Yes?" Rabbit prompted.

"I saw Neo die. He was killed by someone he knew, someone he called a traitor. It felt so real, that's all." She took another sip.

"That doesn't sound too bad," Rabbit assured her. "Cheer up, it's just a dream. We've got a meeting to attend."

The _Nebuchadnezzar _flew through the tunnels of the past civilization's sewers. Voyd, the new Operator, sat anxiously in his chair and watched as Morpheus steered haphazardly around large rock formations and through the smallest openings. The gunner, Phoenix, sat idly nearby, flipping a coin into the air and catching it before it hit the ground.

"We're late," Phoenix reminded his captain.

"I know," Morpheus replied. "We're almost to a safe broadcast point."

Sentinel activity had been rapidly increasing in the five months since Neo had been unplugged. It was almost impossible now to find a safe broadcast point. In the one month Voyd had been operating onboard the _Neb, _he had seen three missions interrupted by Sentinels. Fortunately, no one had died.

Yet.

The sound of an alarm jolted Voyd out of his memories. The holoprojector showed three Sentinels swarming right at the _Neb. _Phoenix jumped out of his chair. 

"Hot damn!" he yelled, rubbing his hands together eagerly. 

"Finally, some action," he continued, sliding into the gunner's seat. Phoenix had always been this way, as long as anyone could remember. He had been on three ships before the _Neb, _being transferred each time after a particularly reckless stunt. Once he even had gotten fellow rebels killed. That had been on his last ship, the _Logos._ Then Phoenix had been transferred here, for what Commander Locke had called his "last chance."

Phoenix had bright reddish hair and numerous freckles, and those attributes in part led to his name. He was rather tall and gangly, with piercing black eyes, which were described by his last captain as "calculating and cold." The years of fighting showed on Phoenix more clearly than many others.

And those many years had paid off. Phoenix was one of the most accurate rebels in the fleet. He had trained with Ghost for a month before being transferred, and had learned well. He brought up the targeting computer, centered his brackets on the first Sentinel, and fired.

The machine exploded in a burst of flame. The other two separated and each came at the _Neb _from opposite directions. Phoenix shifted his focus to the left and fired off another round, striking the second Sentinel directly in the head. The machine crashed to the floor.

The third Sentinel darted in close, too close for weapons. Phoenix fired anyway, but clearly missed. The Sentinel raised itself up to attack.

"You missed!" yelled Voyd, reaching for the EMP.

A large boulder came crashing down on top of the final Sentinel. Phoenix smirked.

Niobe, commander of the _Logos,_ dropped the papers onto the table. 

"These geotherms confirm the last transmission of the _Osiris. _The machines are digging."

Murmuring ran throughout the room.

"They are boring straight down from the surface to Zion."

"They'll pass all the perimeter defenses!" cried a shocked Ice, captain of the _Gnosis_. 

"How many are there?" inquired another rebel more calmly.

"About a quarter of a million," answered Ghost, Niobe's partner.

"That can't be right," muttered Ice disbelievingly.

"And why not?" asked a new voice. "One Sentinel for every man, woman, and child in Zion. That sounds exactly like the thinking of a machine to me."

Morpheus walked into the room, followed by Neo, Trinity, Phoenix, and Lynx, most of the crew of the _Nebuchadnezzar. _The other two crewmembers, Fallen Angel and Rabbit, had already made there way inside and greeted their friends with a now.

"Captain Morpheus," acknowledged Niobe, while she shot a cold look at Phoenix, who was hanging near the back, avoiding the glances of Ghost and his former captain.

"Niobe," Morpheus replied. He continued talking to the gathered rebels. Neo suddenly had a strange feeling. "What is it?" asked Trinity. He only motioned for her to remain downstairs as he went up.

A knock on the door startled Tyger out of his reprieve. He opened the viewing slat to see only a darkened face, guarded from view by bright headlights from behind. 

"I'm looking for Neo."

"Never heard of him," answered Tyger.

"Will you give him this?" asked the face, handing over a package. "You see, he set me free."

"Fine," answered Tyger. "Now piss off."

At that instant Neo came up the stairs. 

"What did he want?"

"How did you know someone was here?" asked Tyger, handing over the package.

Voyd glanced at the screens in alarm. He wasn't ready for anything this big. He had only gotten this job last month! Better call someone and warn them…

Voyd was one of the Believers. When Captain Morpheus had returned the Zion and announced he had found the One, many rebels had flocked to join up with him. Few had been accepted. At first, Voyd had not, because the _Neb _already had an Operator. But after Tank had died in a Sentinel attack, Voyd had eagerly re-applied and gotten the job.

Voyd had long, black hair that hung down to his shoulders. His eyes were also jet-jet-black. At all times he had an expressionless face, no matter how he felt inside. He appeared calm, but he was boiling with turmoil on the inside as he dialed Lynx's number.

Neo looked up at Tyger. 

"Get out of here," he ordered. "Agents are coming." Tyger asked no questions, just took off for the basement to warn the others.

Lynx's phone rang. It was Voyd.

"What is it?" she asked, worried about what would make her lover interrupt an important meeting.

Morpheus was asking one of the rebels to stay and wait for a message from the Oracle. Lynx turned around and walked away a bit to continue the conversation.

Lynx was another veteran fighter. She was one of few rebels who had been fighting as long as she had without inheriting command of a ship. She simply had no ambition too command, she told others. The truth was she would not order fighters off to their deaths. Lynx had transferred to the _Neb _to fight alongside the legendary Morpheus at first, but later had come to believe in Neo. 

Lynx had long black hair that fell past her shoulders, and dark brown eyes. She stood above average female height, and was thin and agile. Lynx wore a black shirt and black leather pants, along with a black cloak. At her side were two pistols.

"There are soldiers coming your way. And they've staked out the sewers. You guys will have to fight your way out. Good luck."

"Shit. Thanks for the warning." She hung up.

"The Calvary has arrived, ladies and gentleman," announced Lynx. At that moment, Tyger ran down the stairs. "The Feds are here!"

The crowd of rebels broke for the exits. Trinity turned to Morpheus. 

"What about Neo?"

"He can take care of himself," answered Morpheus. "We're gonna split up. I'll take Rabbit and get to the streets. Trinity and Lynx, you two put your considerable talents to use and assist our fellow rebels. Phoenix, I think it's time for you and Fallen Angel to have some male bonding time. Let's go, troops."

Lynx smiled. She could see why Morpheus was one of the most loved rebels - his choices showed excellent consideration. He would be able to watch over the weakest fighter of their crew. Phoenix and Fallen Angel's fighting styles - gunplay and hand to hand, respectively - complemented each other perfectly. And Trinity, well, Lynx had never really gotten along with her. She had the feeling the older woman didn't like her. Maybe their first "real" battle together would bring them closer.

There was a banging on the door, and three Agents, Jackson, Hewitt, and Levine stood in the doorway facing a calm Neo.

"The Anomaly," stated Levine.

"Should we proceed?" asked Jackson.

"Yes," replied Hewitt. "He is still,"

"Only human."


	2. The Escape

**

Part One: The Rebellion

**

_"The path of the One is made by the many."_****

* * *

**Chapter One: The Escape**

Jackson leapt at Neo, slashing diagonally with his open palm in a knife-like move. Neo caught the Agent's wrist and shoved his arm upwards. Using him as a brace, Neo kicked out at the Agent's chest and sent him flying back into the other two, who caught Jackson and helped him stand up.

He brushed dust from the fall off of his suit. 

"This will require more…extreme methods," the Agent said to his comrades. The three came at Neo from different angles. 

Neo blocked a chop from Jackson and kicked out at Hewitt. Hewitt grabbed Neo's foot.

Neo looked surprised. 

"Upgrades?"

Neo grabbed Jackson's arm and swung him around into Hewitt. Levine threw a kick at Neo's stomach but the blow was bated aside by a hand and returned much quicker. Neo's foot struck the Agent, sending him flying backwards into a wall. He hit the stone, left a dent, and fell forward.

The other two Agents paused and glanced at Neo. He causally watched as the defeated Agent's corpse returned to its original form and then turned his head to the remaining Agents.

"One down, two to go," he said tauntingly.

Morpheus crouched at the mouth to a sewer pipe. He heard footsteps splashing along and gunshots echoing behind. Ghost appeared, but he slipped on the wet surface and went sprawling, leaving his cell phone in the pipe as he fell to the ground below.

Rabbit grabbed the phone and tossed it down to him. 

"Catch!" Ghost received the throw and saluted with it gratefully. Then he continued along.

Morpheus motioned Rabbit quiet. They heard footsteps coming down the tunnel again, but these were much slower and much more numerous. The duo heard three voices conversing in hushed tones.

_"He went this way, I'm sure of it," _said the first.

_ "I'm telling you, I heard someone else down here!" _said a second, deeper voice.

_ "Shut up, you're gonna give us away," _ complained a third.

_ "This is stupid. Why do we have to guard a damn phone?" _asked the second man.

_ "Because the Powers That Be told us to," _ the first voice replied._ "You complain, it's your ass, not mine - "_

The last speaker ended in a yell as Morpheus shot his foot out to connect with the side of his head. Morpheus instantly saw they were in for a fight. Five SWAT with full body armor and weapons traveled down the pipe, not counting the one Morpheus had already knocked cold.

Phoenix watched a group of three guards run past him towards the hard line. He peaked out, put his sniper rifle to the eye, and shot the lead man right in the back of his neck. The other two whirled around, and Fallen Angel leaped from behind, catching one in a tackle. The third man ran to help his partner, but was shot between the eyes by Phoenix.

Fallen Angel hit his opponent with a vicious punch to the neck, then wrapped his legs around him and started pummeling him. Phoenix ran and grabbed Fallen Angel by the wrist, and the other rebel almost hit Phoenix before stopping himself.

"Calm down," suggested Phoenix. "He's done."

Ghost from the _Logos _jogged up. Ignoring Phoenix, he waved to Fallen Angel and grabbed the ringing phone. Ghost disappeared.

Fallen Angel noticed Ghost's treatment of Phoenix and turned to look questioningly at him. Phoenix sighed. 

"I used to be on his ship and was transferred for reckless behavior."

Fallen Angel clearly wanted more explanation, but Phoenix shook his head. 

"Later. Now is not time for a discussion like this."

Fallen Angel shrugged and reached for the phone as it started ringing. As his hand touched the receiver, there was the sharp crack rifle and the phone burst into pieces, the bullet going clear through his hand. Phoenix whirled around to search for the assailant.

Lynx heard footsteps pounding along below the elevated catwalk that she and Trinity sat on. Looking down, she spotted Niobe and Ice fleeing from a group of ten or twelve SWAT. Lynx dropped to the floor, her cloak billowing out behind her, and brought her two pistols up, squeezing off a shot from each. One man went down, the second target surviving because of thick body armor.

Trinity jumped, landing atop a third man. 

"Niobe! Ice!" she called. "Stand and fight!" The two captains complied.

Niobe stopped suddenly and sent her foot back into her pursuer's head, twisting it around with a sickening crack. Ice jumped to a wall, pushed off it with her left foot, flipped back, over a SWAT, and landed behind him. Ice's fist shot straight forward, pushing the man's chin down into his neck at astonishing speed. He collapsed to the floor.

Lynx dropped her pistols and ran to the man she had downed. She dove and grabbed his weapon as his partner opened fire. Holding the gun in one hand, she used the other to propel herself into the air while squeezing the trigger. The man jerked as the bullets hit him and fell to the ground, blood coming out from his mouth.

The remaining six men formed a tight circle with their guns pointed outwards.

Morpheus dove forward and rolled, launching himself feet first into one of the oncoming soldiers. Rabbit kicked out at the one beside him, but his foot was caught and the soldier pushed him to the ground. Rabbit's head struck the cold metal with a thud, and he saw stars.

Morpheus quickly moved to the third man and dispatched him with a quick elbow to the throat. The fourth and fifth men, however, being ready, proved more of a challenge. Not wanting to risk hitting their comrades, they did not open fire but moved to engage in hand-to-hand combat with the infamous rebel.

The first attacker swing at Morpheus with his rifle. Morpheus grabbed the rifle and twisted it sharply up, breaking it in two. The man gaped in horror as Morpheus reversed the severed barrel and jammed it into the man's throat.

Rabbit's attacker kicked his prone form in the stomach. Rabbit winced in pain, his fingers scrabbling for purchase. They closed over the defeated man's assault rifle. Grimacing in pain, Rabbit brought the weapon around and opened fire, sending his attacker to the ground.

The fifth man fled back down the tunnel. Morpheus extended a hand to Rabbit and helped him up. 

"You okay?"

Rabbit winced. 

"I think the bastard cracked one of my ribs."

Just then, they heard a strange sucking sound from the direction the last SWAT had fled. Rabbit, recently unplugged, glanced at Morpheus curiously. Morpheus, a veteran of many battles, had heard the sound before. 

"Run!" he cried, dashing down the pipe in the opposite direction of the sound.

Hewitt and Levine came at Neo again. Neo blocked a closed-fist blow from Hewitt and moved his arm around the Agent's fist, grabbed it, and flipped the program over to the ground. With his other hand, he blocked a similar move from Levine, thrust the Agent's arm away, and punched him hard in the chest. Levine stumbled backwards.

Hewitt scrambled to his feet and joined Levine. Levine grabbed a nearby sign post and broke it in half, handing the other half to Hewitt. Neo eyed the new makeshift weapons. This could be harder than he had at first thought.

A figure stepped out of the shadows. He was tall, wearing a pure white suit. He had long, white dreadlocks that hung down to his shoulders. He wore dark sunglasses.

Phoenix gaped. Cleary not an Agent or human, but what was it? His astonishment continued as a second one, exactly identical to the first, stepped out beside him.

"They are not the primary target," said the first.

"But they associate with him and work against our master. They must be eliminated."

"We will do it."

Phoenix raised his gun and shot at the first figure, whose body went clear. He faded to an outline with a whitish tint, and his hair rose above his head like the Medusa of lore. The bullet passed harmlessly through him.

"Destroy them."

The two figures charged. The first leapt up into the air and landed in front of Phoenix. He punched and Phoenix bent backwards to dodge, the man's fist going over Phoenix's chest and past his head. Phoenix turned his dodge to a flip and lifted the…ghost…up with his feet, catapulting him over the railing behind the combatants. The ghost fell, grabbed a railing that stretched across the chasm below, flipped around it, and shot back up to the platform, landing in front of Phoenix.

The second ghost kicked straight at Fallen Angel, who was still holding the ruined phone. Fallen Angel took the phone cord, wrapped it around the ghost's foot and yanked, causing the ghost to spin around in midair and fall to the ground. Fallen Angel moved to kick the ghost's form when the ghost drew a knife and stabbed it into Fallen Angel's leg. He grunted and bent over, tearing the knife from his leg. The ghost rolled away from him and leapt to his feet with catlike agility.

Fallen Angel turned to Phoenix. 

"This could be harder than we first thought."

Lynx, Trinity, Ice, and Niobe ducked behind a nearby pipe as bullets filled the sky around them. They looked at each other.

"I'll take them," Lynx said.

Ice looked at her in shock. 

"You can't possibly take down six soldiers with weapons yourself!"

"Watch me," she replied, standing up.

Niobe moved to grab her, but Trinity stopped her. 

"I'm coming too," Trinity said. "Ice is right."

Lynx rounded the pipe with both pistols drawn. She was calm, centered. Her tutor's voice filled her mind.

_Free your mind._

The air filled with bullets once more. Lynx dashed to the left. Time seemed to slow down for her. She ducked under one bullet and pushed off the ground and jumped over another one. She twirled her pistols and fired, jumping to the side at the same time.

She hit the ground and rolled into a crouching position. Flipping forward, she sprang into the group of soldiers. She took hold of one man's rifle and jammed it up, bringing the butt of the weapon into his chin. Then she whipped the gun around, smacking it into the face of the next man.

Lynx opened fire. The bullets tore through the air, killing two of the SWAT men. Lynx side-kicked at the man across the way, sending him sprawling backwards and over a railing. She dropped the gun and turned around, seeing the last man holding an assault rifle and bringing it to bear. He opened fire. One bullet shot forward and hit her in the stomach. The man walked forward and pointed the gun at her head. A gunshot rang throughout the arena -

- and he dropped dead from Trinity's quick shot.

Rabbit peered over his shoulder and glanced at the figure pursuing them. An Agent. 

_Holy Shit!_ Rabbit thought, turning on the speed. His legs pumped up and down, and his footsteps echoed throughout the sewers as he ran as fast as he could. 

_I wasn't made for this…I'm a hacker, for crying out loud! Someone save me!_

Morpheus fired a shot back over his shoulder at the Agent. The Agent stopped to dodge the bullet, and the rebels got an extra lead. Rabbit heard a phone ringing past the railing again. Morpheus came alongside him.

"When we get to the railing, jump!"

"Hell no!"

"Trust me!"

Rabbit would have protested again, but he reached the railing at that moment. Morpheus vaulted over the side, and Rabbit thought _what the hell _and followed.

He hung in the air a second before falling. He hit the catwalk below and rolled, coming up before a ringing phone. _Thank God…_ he thought, grabbing the phone and listening to the voice.

"If you would like to make a call, please hang up and try again. The following tones are for the hearing impaired."

"Son of a _bitch_!" cried Rabbit, dropping the phone. Jackson landed on the platform behind the two. Rabbit glanced around. Nowhere to go. No way out. A true dead end.

Ghost One leapt at Phoenix, jumping high into the air with a kick aimed at Phoenix's head. He slapped One's foot to the side and flipped over backwards, bringing his feet into One's back. One tumbled to the floor, but managed to fall into a roll and spring up on the opposite side of Phoenix. Phoenix swung his foot around in a roundhouse kick, but One just phased, and Phoenix's foot passed harmlessly through.

Ghost Two was more subtle. He stalked around the edges of the platform, watching Fallen Angel closely. Fallen Angel took his time also. He bent to the ground and picked up the phone. He yanked it out of the wall, the cord coming with it, forming a crude morning star-like weapon. Two suddenly exploded in a fury of motion. His arm went to his side and snapped back out, a dagger glittering in the dark sewer air. Fallen Angel snatched the dagger out of midair and hurled it back at Two, who phased as it passed harmlessly through him.

One grabbed Phoenix's foot as it completed its pass through One's ghostly form. He tugged the foot forward, bringing Phoenix in close. Phoenix brought his other foot up to connect with One's face, snapping his head up and knocking his glasses off. One grabbed his face and dropped Phoenix, who landed on the floor.

Fallen Angel swung his weapon at Two. Two flipped backwards, grabbing his knife before landing on his feet again. He darted in close to Fallen Angel, but the phone brained him on the side of the head before he could phase out of its way. Two darted in again, and Fallen Angel swung the phone in retaliation, forcing Two back.

Two faked an attack, and then grabbed the phone as it was swung. He hauled it forward, snatching it from Fallen Angel's grasp. He ducked under a kick and slashed his knife upwards across Fallen Angel's chest, leaving a trail of red from hip to shoulder across Fallen Angel's white uniform.

The pain overwhelmed Fallen Angel. He sank to his knees, clutching his stomach with both hands. Two walked forward and slashed up Fallen Angel's face, lifting the freedom fighter up and laying him out flat. Two knelt down for a killing blow -

- and sank forward onto his own knife when Phoenix stumbled backwards onto him.

Two flipped up and phased, his wound instantly healing. "Just like new."

"We owe you for that," said One somberly.

Just then, the two put turned their heads, listening. They turned to each other. 

"The primary target. We must go."

They turned to the rebels. 

"We will meet again." 

They disappeared over the side.

Trinity ran forward and knelt down by Lynx's form. Blood was slowly seeping out in a circle from the gun wound. Lynx was staring off into space, a feverish look on her face.

"So cold," she muttered. Trinity shook her. 

"Stay with me, Lynx," she pleaded. The young woman had become a friend in the last months, even the Trinity had never shown it. Supporting Lynx on a shoulder, they continued towards the hard line.

Neo took a step back and grabbed part of the stair railing. He concentrated on the code for a second and then removed a section shaped like a perfectly proportioned staff. Hewitt swung at him and he deflected the attack with one side, bringing the other around and hitting Hewitt in the stomach. He returned the first side to Hewitt's head, moving to fast for even the third-generation Agent. Hewitt sank to the floor, defeated.

Levine fled back down the alleyway from which he had come. Neo changed the code again and threw the pole. With its new sharp end, it went straight through the fleeing agent. Neo looked around the alleyway.

_Now what?_

He concentrated for a moment, the ground rippling our beneath him, then took off into the sky.

Supporting himself on Phoenix, Fallen Angel slowly and laboriously made his way to a hard line. The phone rang, and Fallen Angel gratefully picked up the receiver. He put the line to his ear and disappeared. Phoenix hung up the phone and waited for the call. When it came, he exited the Matrix with one simple motion.

Jackson opened fire. Rabbit dove to the floor, but he was not the Agent's primary target. Morpheus dodged all the shots and returned them even less accurately, the Agent moving so fast it seemed like there were five of him.

The Agent closed in, herding Morpheus into a corner with a series of powerful punches and kicks. Morpheus swung high, and Jackson grabbed his wrist and dragged Morpheus's leg across his own, sending Morpheus to the floor. Morpheus rolled off the edge, grabbing on with two hands. The Agent walked forward, foot poised to crush the rebel's hand, and snorted. 

"Humans."

"Programs," sneered Rabbit, shooting the Agent in the back. He whirled around, gun coming up, and Morpheus grabbed his leg and pulled him off the cliff. He helped Morpheus up and they walked back to the phone. It rang.

"After you, Captain."

Morpheus left, and Rabbit followed.

Trinity lay Lynx down in front of the hard line. It rang almost instantly. Trinity smiled. 

_Voyd's watching over her. _Trinity grabbed the phone and brought it down to Lynx's ear.

Lynx woke in the _Nebuchadnezzar. _Voyd rushed over to her. 

"Are you all right?" he inquired anxiously. Morpheus grabbed him by the shoulder.

"We'll take care of her. Not everyone is out, Operator." 

Grudgingly, Voyd returned to his seat.

"Greetings, Miss Raines," said Hewitt, as he walked towards Trinity. Trinity glanced back at the destroyed hard line. She could faintly hear a ringing from further down the tunnel, but first she had to deal with the Agent.

Niobe and Ice came up quietly behind the Agent. Trinity nodded at them. Hewitt rushed forward and slashed at Trinity with his fist. She blocked the blow and jumped into the air, kicking him in the chest. He stumbled backwards-right into Niobe. Niobe hit him in the face, sending him sprawling to the ground a foot away from the railing. Ice rushed over to him, but he kicked out at her ankle and sent her flying.

Niobe, rushed forward. She swung down at the Agent, who blocked her blow high and fired his gun into her stomach. Niobe sank backwards to the floor. Trinity took out her own pistol and fired as quickly as she could, barley touching the Agent's left leg. She turned and looked behind her as she heard more footsteps coming up behind her.

Levine appeared from the other direction. 

_Shit!_ thought Trinity. The odds were too great now. Trinity dashed forward, avoiding fire. She ran for the railing and leaped into the darkness, the Agents firing after her. She landed on a platform and grabbed the ringing phone, putting it to her ear.

After Trinity finally came out of the Matrix, she walked over and stood beside Voyd, at the operator's chair. 

"Where's Neo?"

"He's doing that Superman thing," said Voyd, pressing a button to show her. Trinity watched for a second and then turned away to find Morpheus.

Neo soared through the clouds, losing himself in the joy of flight. After a hard battle, it was always what he did to unwind. 

_The Matrix isn't _all_ bad_, he thought to himself. _It's control that is the problem. If we told people the truth, many of them would want to stay, even if they knew they were under control. If we destroy the machines, maybe we can make the Matrix a paradise for us._

Ice looked up as footsteps approached her. A strong hand descended and lifted her to her feet.

"Thanks," she told the rebel.

"Don't thank me yet," the rebel replied, firing her gun twice into Ice's stomach.

He was sitting in the kitchen, idly sipping some coffee. Nearby, Fallen Angel was wrapping a bandage around his hand. There was already one on his throat and chest.

Trinity sat down across from Morpheus. "Who'd we lose?" she inquired.

Morpheus sighed. 

"We were lucky. No one died, but Lynx and Fallen Angel are badly hurt. The other rebels were less lucky. All told, Ice, Tyger, Frost, Ajax, Malachi, and Bane were killed inside the Matrix. And Ballard still might die from his injuries. The worst part is, after this fiasco, no one will stay and wait for the Oracle."

"Then what are we going to do?"

"I guess we'll stay here ourselves and get Lock's orders via communication. It wasn't necessary to go to Zion anyway. It'll just be another week. Niobe has agreed to recharge our ship before we head back, so it should be fine."

Voyd entered the small room he shared with Lynx and walked over to her bed. There were bandages wrapped around her stomach, and the blood-soaked shirt had been torn away there. Voyd touched the bandages softly, but Lynx woke with a small gasp of pain.

Voyd yanked his hand back. 

"Oh, God, I'm sorry, Lynx-"

She smiled, calming him. 

"It's fine, it's not too bad."

Voyd looked at her. 

"Liar," he accused fondly.

She tiredly nodded her agreement. He grinned, but then got more serious. 

"Listen, Lynx, what you did in there was incredible. But you were still hurt badly. Please, never do _anything _like that again. Promise me."

Lynx sighed in exasperation. 

"Voyd, we've gone over this before. You know I can't do that. This is a war. I'm a soldier," she told him, mimicking one of Morpheus's sayings. "I'll make it to the end, too," she confided in him. "I know it. Then we'll have all the time together we could want."

"But when will the war end? 20 years?"

"No," Lynx answered. "Morpheus and Neo are confidant, and I believe them, that it will be within the month."

"Fine, but I still think-"

"Oh, shut up," ordered Lynx, bringing Voyd into a kiss.

Phoenix sat in the cockpit, surveying the old sewer system for any possible danger. Morpheus had told him the plan, and while it offered plenty of excitement for the hot-blooded rebel, he also knew one thing.

Locke was gonna be pissed.


	3. Preliminary Excersises

**Chapter Two: Preliminary Exercises**

The three Agents stood on the highest floor of the tallest building, surveying the sprawling city below. The sun was rising, and the sunlight beaming straight onto them would have been blinding if not for the identical sunglasses they wore.

Hewitt turned to Levine. "The anomaly defeated us."

"Yes, he did. But the mission was a success."

"How so?" Jackson asked their leader.

"Many rebels were killed, including a captain. The rebel that contacted us earlier contacted us again, bringing a slain captain as proof of her intentions. Their careful plans were ruined."

"What plans?"

"They wait for contact from the Oracle. The ship assigned to stay suffered heavy losses and left. Only the anomaly's ship remains."

"Are they inside the Matrix?"

"Two are at all times."

"Who is inside right now?"

"The ones they call Phoenix and Fallen Angel."

A cardboard copy of an Agent popped out of the ground. There was a gunshot and its head became a bullet hole. Another Agent popped up across the floor, and Phoenix flipped forwards and shot through it. The cardboard copy fell to the floor.

Phoenix walked out of the training room and made his way to where Fallen Angel sat. He plopped down beside the silent rebel and waved his hand in front of Fallen Angel's closed eyes. Fallen Angel shot his hand out and snatched Phoenix's wrist. He opened one eye.

"Don't do that."

"Sorry," Phoenix said unapologetically. 

"No you're not," Fallen Angel accused, and Phoenix nodded good-naturedly.

"So the Oracle, huh?" Phoenix began. "I remember the Oracle. Scary woman. Do you remember her?"

"Yes."

"What was she like with you?"

_ He had still been Angel then. It was years ago. His captain and lover, a strong-willed woman named Tsunami, had led him to the Oracle's apartment and stopped in front of the door._

_ "There's no turning back now," she had warned him. "The choice is yours. I cannot make it for you."_

_ Angel opened the door. A tall black woman had met him and led him into a room filled with children. Angel sat down beside a young, bald-headed boy bending a spoon. The boy had turned to him._

_ "Do not try to bend the spoon, that's impossible. Only, instead, try to realize the truth. There is no spoon."_

_ Angel concentrated. The spoon had bent. Then it had snapped in two. Looking back years later, he had realized it was an omen. At that moment the woman had summoned him into the kitchen to meet the Oracle._

_ It was not what he had expected. A rather short woman, smoking a cigarette, was sitting at a table. She offered him a seat, and he accepted. As Angel stared across the table at the Oracle, he suddenly had a sense of overwhelming disaster._

_ The Oracle had faced him clearly and greeted him. _

_ "Welcome, Angel. Welcome to my humble home." She had laughed at that before continuing._

_ "Well, you have finally realized the truth. I knew it the day I saw you playing on the street outside your front door. You are slated for greatness. You have a chance, Angel, to be the one of the best. You will have to make a choice, though, before this dream becomes a reality. Poor Tsunami."_

_ "What?" Angel had asked._

_ "Though I guess it is a small consolation that she won't live long enough to realize how bad it will be."_

_ "Tell me," Angel had insisted._

_ "If you insist. You will have a chance to become a captain, the best of them all, and one of the most honored rebels. But you will throw it all away for the sake of a greater ambition. And you will change your name to something much less."_

_ Angel had been very shaken. He had remained quiet until after he had left the apartment. Tsunami had cornered him in the hall and asked him about the visit. He brushed her off by saying it was nothing, just the inane ramblings of an old fortune teller._

_ It was a year before he was proven wrong._

"She was," Fallen Angel replied, lost in thought, "correct."

The only door into the room swung open and another Agent entered. Levine raised his hand in greeting. 

"Agent Matthews."

Matthews nodded his own greetings. 

"Agents Levine, Hewitt, and Jackson. Greetings. I bring word from the Motherboard."

"What does she order?"

"Levine and Hewitt, report to Room 303 for an upgrade. Jackson, report to Room 101."

The Agent's eyes grew wide. He stumbled backwards and braced himself against the wall. 

"No," he whispered in horror.

"Yes," Matthews confirmed. "You are now obsolete. Due to your quick loss to the anomaly and failure to destroy your secondary targets, it has been determined that you will be replaced with a newer model who has increased capacity for advanced battle tactics."

Jackson suddenly drew his gun and shot out the window. He ran and dove out the hole he had made, landing on a building many floors below. The three other Agents looked out at him, but yanked their heads back in when he fired at them. He broke into a run, yanking his earpiece out and flinging it to the ground.

Matthews turned to the other two. 

"Report for your upgrades."

"And Jackson?"

"He is of no consequence."

Voyd sat idly staring into the Matrix code, watching Fallen Angel tutor Phoenix in hand-to-hand combat. It was pretty boring. Voyd was drifting off to sleep when the message bell rang. He pressed a button and Commander Locke's visage filled the screen.

"Holy shit," said Voyd, taking in Locke's extremely annoyed expression. "I mean…I'll just get Morpheus, sir," Voyd assured the commander, dashing off to fetch his captain.

Morpheus slid into the communication seat slowly, summoning his courage for the upcoming battle of wills. 

"Greetings, Commander," he began.

"Don't 'greetings' me, Morpheus. Why the hell aren't you back in Zion yet?"

"I decided that - "

Locke slammed his hand down. 

"You decided? _You _decided! I'm the commander of this army, and I make the decisions. I gave you a direct order to return to Zion - "

"We need a presence inside the Matrix to await contact from the Oracle."

"I don't want to hear that _shi, _Morpheus! It's too dangerous. The Sentinel patrols have increased tenfold in the past two weeks alone! The Agents have stopped fifty percent of the last twenty operations we've ran. And, in case you forgot, there's a goddam army coming right at us!"

"With all due respect commander, there is only one way to save our city."

"And what is that?"

"Neo."

Phoenix and Fallen Angel faced off in fighting stances. Fallen Angel bowed down and Phoenix followed suit. He rushed at Fallen Angel and kicked at his side. Fallen Angel grabbed Phoenix's ankle and pushed off of it, hit his feet on the wall, and cartwheeled over Phoenix, making the rebel flip over and land on his back. Phoenix pushed himself up with his hands and faced off again.

"You are arrogant, Phoenix," Fallen Angel told him calmly. "And that is why you lose. Learn to accept that someone might be better than you, and you have a better chance at winning."

Phoenix sent a punch Fallen Angel's way, but Fallen Angel just batted it aside and slashed his hand across Phoenix's shoulder. Phoenix lifted his other arm and smacked the attack away, then brought his left leg up into Fallen Angel's side. Fallen Angel jumped over the feeble attack and brought his foot to meet Phoenix's head with a thud. Phoenix sagged sideways and grabbed Fallen Angel's foot, bringing him down at the same time.

Hewitt plugged the jack into his ear piece and gasped-something he picked up from the humans-as the upgrade hit him. New information flew into his brain, advanced fighting techniques, logic upgrades, a tactics program, and, most importantly, a tracker that showed the positions of any rebels who stayed in the Matrix for more than two hours. 

There were three dots now - two right next to each other, one inside the Mainframe building itself. Hewitt and Levine headed for the two rebels.

With an understandable amount of trepidation, Jackson knocked on the door that was home to the third most powerful program in the Matrix. A man answered the door. He wore only tight pants and now shirt. His black hair was totally messed up, and he had two long, sharp fangs.

"Agent Jackson," he growled. "We've been expecting you. Come this way."

The servant led the former Agent through a large hallway and into a large office. Behind the desk sat a man, his feet casually propped up on his desk. He spread his hand apart.

"Welcome, Mister Jackson, to my humble home. I understand you wish to join us?"

"Yes."

"And why is that?" inquired the Merovingian.

"I do not wish to be deleted."

"A noble goal, one we can all identify with, I am sure. And we could always use a former Agent. We'd be happy to have you, but first, I must apologize."

"For what?"

"I must test you - "

Jackson leapt up from his chair and squared off in a fighting pose. Three of the Merovingian's servants had crept into the room and were circling him now.

Fallen Angel jumped when the hard line rang. He picked it up. 

"Yes?" he asked.

Fallen Angel vanished from view. The phone rang again, and Phoenix picked it up, put it to his ear, and disappeared.

The first man rushed in at Jackson. Jackson put his foot under the chair he had been on and shot it out at the man, knocking him backwards. He caught the chair as it returned and swung it behind him, knocking the second werewolf back. The third leaped on Jackson's back and bit his neck. Jackson grunted in pain and slammed the chair into his face, knocking him cold.

The Merovingian applauded slowly, almost mockingly. 

"Very good. Come with me."

The Merovingian led the exiled program threw a twisting maze of corridors to a large underground cavern. In the center of the cavern was a small cup of wine. The Merovingian picked the cup up and handed it to Jackson.

"If you really want to join us, drink this program."

"What's it do?" asked Jackson curiously.

"It will permanently separate you from the Mainframe. The process will change you somehow, like it did the Twins. They used to be Agents, you know, during the second version of the Matrix."

Jackson shrugged and drank the wine.

Jackson felt a hot pain shoot through him. His body collapsed, leaving his naked code hanging there, exposed. Jackson felt his code shifting, rearranging.

Jackson opened his eyes.

Voyd answered the phone. 

"Is this the _Nebuchadnezzar?_" asked a heavily accented voice.

"Maybe," Voyd answered suspiciously.

"Give me the phone," ordered Morpheus. "Hello?"

"Send Lynx in," the voice continued. "The Oracle needs to see her."

The man hung up.

He stood in the underground cavern, the Merovingian looking at him. 

"Well?" the Exile asked.

"What?" inquired the fallen Agent.

"How do you feel?"

"Free," answered the rebel hunter, grinning evilly.

Lynx awoke within the Matrix. She drew both her guns and searched the rooms. She felt a hand on her back and whirled around to see a small, Asian man dressed in a white suit with a black undershirt.

"My name is Seraph," he told her. "I can take you to see the Oracle, but first I must apologize."

"For what?"

Seraph put his hands together and bowed slightly. 

"For…this."


	4. Upgrades

**Chapter Three: Upgrades**

Jackson gasped and dropped to his knees. There was suddenly a searing pain in his back. He felt his skin stretching and _ breaking_. There was a ripping sound, and wings shot out of the former Agent's body. Jackson glanced down at his hands and saw his immaculate fingernails lengthening into sharp, deadly claws. He felt a pleasant, burning sensation in-between his lungs. He coughed and fire shot out of his mouth, scorching the ground below Jackson lifted up his left hand and clenched his fist.

The Merovingian reached down to help him up. 

"Well," the Exile began, "you must choose a new name."

Jackson thought for a moment, and then it came to him. 

"Lucifer."

He heard a slow, mocking clap, and in walked the last person Jackson had ever expected to see in the Chateau.

Seraph leapt up, shooting his feet out in opposite directions and kicking Lynx's guns out of her hands. He shot out his hand in a blow towards Lynx's head. She threw up her hand to block it and returned a lightening fast blow at the side of the Guardian's head.

He blocked the blow and shot his left foot out to her stomach. His kick connected with her injury, and Lynx's eyes watered in pain. She dove over Seraph and landed behind him. Whirling around, she blocked a blow from the man and kicked out at his knee, connecting with a solid crunch. Seraph flipped over backwards and she dove after him, swinging her fist into his jaw. He shot his palm into her chest and shoved her backwards.

She ducked behind the remains of one of Phoenix's practice targets. Seraph's fist shot through the stomach of the replica and she stepped on it, using his arm as a brace and jumping into the air above his head.

Voyd watched the screens in amazement. Lynx's code was glowing furiously. Voyd had never seen her move so fast and hit so strong. He watched her continued fight against the Guardian with astonishment.

"Wow," he whispered almost silently.

"Mister Jackson…" Smith said in a drawling tone. Lucifer gazed at his former leader in astonishment.

"You are undoubtedly wondering how I am still here."

Lucifer nodded mutely.

"I _was_ deleted. The anomaly managed to neutralize my code, through an old-fashioned process I was unprepared to defend against. That problem has been solved. And now I live for only one purpose."

"And what is that?"

"To destroy the anomaly."

Phoenix glanced over his hand and his eyes moved to Fallen Angel. 

"Your play."

Fallen Angel looked up in irritation. 

"I'm fully aware of that. Now if you would just wait for twenty seconds past your diminutive attention span then maybe I could get some thinking accomplished!"

Phoenix smirked. Fallen Angel selected a card and placed it down on the pile. He dropped his hand to the ground. "I win."

Phoenix cursed. 

"Not again!"

Voyd ran in. 

"Hey, guys, stop the games for a moment. There's a situation."

Lynx aimed a double kick at Seraph's head. Seraph blocked her blow with his arms and flipped over backwards. The two combatants landed at the exact same time and squared off into fighting stances.

Seraph relaxed his stance and bowed. 

"Good. This way."

Lynx blinked a few times behind her shades. _ What?_

She gave a mental shrug and walked after the man. Seraph led her to a door in the adjoining room. He opened it, revealing a white hallway with many green doors. Lynx stepped through the portal and shut the door behind her.

Voyd jumped in his seat. "Where'd she go?"

"They're marooned," Morpheus observed. The _ Nebuchadnezzar _slowly approached the powerless _Gnosis_. Phoenix slowly set the hovercraft down next to the ruined ship. 

"Let's move out," the captain ordered. Phoenix grabbed an EMP rifle from the gun case and followed the crew across. Morpheus led, slowly opening the hatch of the _Neb _and glancing around outside. He pressed the radio to his ear. 

"Voyd?"

"Still clear, boss. You're good to go."

Morpheus jumped across the gap between the two ships. He opened the door on the _Gnosis _and walked inside. Phoenix came across after him, and Fallen Angel followed the rebel.

The crew spread out and began searching the corridors. Morpheus headed left, And Phoenix and Fallen Angel walked down the right passageway.

It was Morpheus, however, that finally found the crew.

Rabbit sat on his small bed, typing away on a laptop that was hooked into the main console of the _Neb. _Green coding spiraled down his screen, shifting form and position as he typed. From across the hall, Voyd looked over into the open room.

"What are you doing, anyway?"

"I've written my own Agent program," Rabbit said smugly. Voyd frowned and walked over. 

"What the hell are you talking about?"

Rabbit displayed his computer screen. On it was an Agent, but instead of the business suit and glasses, this Agent wore a fluffy pink tutu and wore star-shaped lenses. His hair was died neon green.

"What is that?"

"My Agent," Rabbit replied, hurt. "I call him Priscilla."

"Why'd you make an Agent?"

"I need to test out my new program on him."

"What?"

"I've written a program designed to destroy the Agents and other machine-controlled programs. I need a test subject."

Voyd stared in shock. A program that destroyed Agents…

"You know what this could mean?"

"No, I don't. I designed it just for the fun of constant frustration, 'cause I get my kicks from failure. Now leave me alone, I'm testing the program."

Rabbit typed in a command and hit send. Both the rebels stared anxiously at the Agent on screen, waiting for something to happen.

"Where are we?" asked Lynx, her voice echoing in the hallway.

"A programmer's back door," the Guardian answered. "These doors lead everywhere in the Matrix."

Lynx looked around her. "How does it work?"

"Each "door" inside the Matrix is in reality a piece of code. All that is needed to change the code's function for a brief amount of time is the correct program," Seraph answered, displaying a key he held in his hand. He put the key in a door and twisted it counterclockwise, opening the door to reveal a teahouse. Sitting at a table, sipping a cup of tea, was the Oracle.

"The recurring versions of the Matrix are becoming more and more flawed. In the first version, when I was newly activated, the anomaly barely lasted two weeks before we lured him to the Source and destroyed Zion. He made the choice, and was neutralized. In the second version, the anomaly almost made the wrong choice.

"Sensing a problem, the Architect rewrote the emotions program once again. The third cycle went off without a hitch. The fourth cycle was a little rocky – an Agent was almost killed – but we defeated the rebellion once again.

"Then came the fifth version of the Matrix. A rebel who called himself "Raven" took down an Agent. The Architect revamped the entire Matrix program in order to make us stronger and more indestructible. It was a disaster. The Mainframe crashed, and we lost entire crops of humans. Power was lost for days, and the rebels wiped out a large portion of our army. However, in the end, we put them down, as always.

"But now they have killed an Agent again, me! I fought against the Source, and was allowed to stay. I pulled myself free of the Mainframe, just as you did here. And now, I am free."

"Welcome back, Lynx," said the Oracle smiling. "Please, have a seat."

Lynx sat. The Oracle smiled again.

"I still remember last time you were here, just after Niobe unplugged you. You were young, headstrong, very determined, and very foolish. You have grown in many ways since then. Now you have become a true fighter."

Lynx gradually grew uncomfortable under the Oracle's examination.

"Why - "

"Are you here?" finished the Oracle. "Simple. Neo is need in the outside world right now, and I need to get him a message. The time has come. The endgame draws near, and unless you rebels can do something to stop it, all will be lost."

They lay in the galley, dead. Five crew members, three men and two women, lay face down one the floor, no marks on their bodies. Morpheus knelt down by one female, a yellow-haired woman, and turned her over. She stirred, and Morpheus jumped backwards. 

Morpheus spoke into his radio again. 

"Voyd, have Neo and Trinity bring a stretcher over here. One's still alive!"

Phoenix examined the black box in the command bridge more closely. 

"It looks like some sort of machine, but I've never seen anything like this in our ship. What's it do?"

Fallen Angel shrugged. 

"Beats me. Cut it open."

Phoenix slipped out his knife. He stabbed the box and dragged his knife along the edge, cutting the top off. He ripped the cover away, revealing complicated machinery. As he was doing that, Fallen Angel searched through the ship's records.

"Hey, I found the ship's log!"

"What's it say?"

Fallen Angel put it on the screen.

_ 00:52:34_

_ Today we lost Ice. The meeting was ambushed, and she failed to get out alive. The funny thing was Digit never _saw _her die. We don't know how it happened._

_ No one knows what to do next. We've been ordered back to Zion, but no one knows exactly where to go. We've decided to put out a radio call for assistance._

_ 05:34:24_

_ Are call was answered by a Sentinel we destroyed it, but not before it got off a radio message. We must flee._

_ 12:45:23_

_ We found the wreckage of another ship, the _ Hammer. _Exploring inside it, Pandora found a black box in the bridge. There was no sign of the crew anywhere. We brought the box back with us._

_ 17:56:57_

_ Pandora decided to open the box. When she did_

"When she did what?" asked Phoenix.

"It cuts off there," answered Fallen Angel.

Phoenix examined the box he had opened. 

"This must be Pandora's mysterious box then."

Fallen Angel looked up in horror. "And you just opened it."

A red light went on inside the box, and a loud, rapid beeping sound filled the bridge.

Priscilla stood there on the screen, looking around. Suddenly, a red spot appeared on his arm. He glanced down in agitation and touched it. It spread to his finger, leaping up his other arm and to his shoulder. He cried out in surprise.

The virus spread over the Agent's body, until the program was covered in the mysterious red substance. Black cracks appeared throughout the Agent's body, and he suddenly collapsed into pieces, falling to the floor.

Voyd and Rabbit stared. 

"It worked," Voyd said shakily.

Rabbit seemed unsurprised. 

"I wrote it, after all."

"And so now we come to a crossroads in fate," the Oracle continued. "For it is the time of the humans. I believe we are closer than any other rebellion has been - "

The Oracle paused and glanced up at Lynx, as if in fear. Lynx shrugged mentally.

A male voice interrupted from behind them.

"You always were a dreamer."

Lynx turned her head to see a tall, bald-headed man dressed in white robes. A beard covered the man's chin, stretching down to his chest. He walked with support of a staff. His black eyes swept over the room, taking in the three occupants. His eyes lingered on Lynx for a moment.

He stepped forward. "Greetings, Prophet." The Oracle said calmly.

_Do not try to bend the spoon, that is impossible. Only instead-_

"Try to realize the truth."

"What are you talking about?" Lynx asked.

_Pain._

That was what Pandora noticed first, the pain. It singled her reawakening into the world of the real. There was a sea of blackness and pain, in which Pandora felt herself floating. She pushed upwards, past the pain and blackness, into a world of confusing light and sound.

"Hold her, she's coming up!"

Her eyes opened. A black man – the legendary Morpheus – was examining the readouts on the medical table. A black-haired woman knelt down besides her, holding her hand and sticking a needle in. And to Pandora's left – a man she recognized very well.

Neo. The One.

"How do you feel?" he asked her kindly.

She thought for a second. 

"It hurts."

The Oracle shot a cautionary look at the Prophet. She opened her mouth to speak, but Seraph laid his hand on her shoulder. 

"It is time."

The Oracle got up and headed to one of the doors. As Seraph opened it for her, she glanced back over her shoulder at the Prophet. 

"Now is not yet the time for your truth."

She looked over to Lynx. 

"Give Neo this message: He must reach the Source. Nothing else matters. When he reaches the Source, the path of the One ends. And so will the war."

The Oracle left the room.

The old door swung open, creaking on its rusty joints. The Key Maker looked up from his ceaseless work to see the shadow of the Merovingian fall across the opening to his small cell. He walked in, flanked by his two bodyguards. The Key Maker got up from his bench and faced his captor boldly.

"Your escape attempt failed," the Merovingian stated simply. "And it has been suggested that your continued existence is a threat to the stability of our little retreat."

"We do only what we are meant to do," said the Key Maker calmly.

"And you are meant for only one thing," the Merovingian replied. "Deletion."

Twin One brought his gun up, pressed it to the head of the Key Maker, and pulled the trigger. Two knelt down and examined the body, pulling a golden key from around the corpse's neck. He handed it to the Merovingian.

The Prophet sighed. "I have been instructed not to reveal all to you. But the Oracle is correct. Neo must go to the Source. Give this to him."

The Prophet handed Lynx a slightly bent spoon. Lynx smiled. He walked to a door and turned the knob, revealing the back doorway again. He stepped through.

The door on the opposite side of the room swung open as the door shut behind the prophet. Through the door stepped the figure of an Agent Lynx had never seen before.

Pandora sat on the edge of the medical table, holding her head. Morpheus passed her an aspirin and a cup of water. "What happened?" The captain asked her.

Pandora swallowed the pill and took a gulp of her water, then began speaking in a trembling voice.

"We found the _Hammer._ It was completely…completely destroyed. No one alive. We also found a black box inside. We brought it back to the ship to see what it did. I decided to open it, and when I did - "

She choked briefly, swallowed, and continued. "When I did, a horde of Sentinels found us. They threw a bomb at our ship and knocked us off course. Everyone died in the crash, except me."

The light beamed brighter, and the beeps increased in volume and frequency. Fallen Angel dropped the box and ran through the door, leaping across the gap between the two ships, Phoenix hot on his tail.

He rushed into the medical bay. 

"Morpheus, we need to leave now. I opened some box, and I've got the worst feeling that - "

Pandora gasped. 

"Get out of here, Morpheus, or we'll all die."

"Miss Hawkins, nice to finally meet you at last."

Lynx kept her guns pointed at the newcomer. 

"Who are you?"

"You do not remember me? I'm hurt, Miss Hawkins."

It dawned on her. "Smith? You?"

"Me, me, me," the Agent answered. Lynx turned to run, but the door behind her opened and another Agent…_Smith!_...stepped through.

"Me too," he said.

Voyd stared. "Run, Lynx, run!"

Lynx opened the third door and ran out into the sprawling megacity that was the Matrix. She heard the sound of Smiths running behind her. A third Smith appeared ahead of her, firing a pistol. She dove over the bullet, rolled, and continued running. She grabbed her cell phone and dialed her ship.

"There's an exit at Franklin and Jefferson. Can you make it?"

Lynx glanced around her. 

"Maybe."

"Good luck. And hurry. Out."

Fallen Angel slid into the driver's seat and powered the ship up. Phoenix dropped down into the gunner's seat. The _Neb_ lifted off and shot out of the cavern, just as Sentinels flew in the other side.


	5. Erasure

**Chapter Four: Erasure**

_ It was happening again._

Pandora shivered in fear. She cold faintly hear (or so she imagined) the humming of a thousand Sentinels pursuing the lone hovercraft through the tunnels of the real world. The sound, a resonant buzzing, filled her head and she thought it might explode from the pain. A trickle of water squeezed its way from the corner of her eye, traveling down her face. The room's only other occupant, Morpheus, looked over at her in surprise.

"Pandora, are you feeling alright…"

His words trailed off as the buzzing grew in intensity. There was a loud popping sound and the blackness rushed up to overtake her.

Lynx felt the air rush past her ear and a bullet struck the pavement next to her left foot. Pivoting on said foot, she turned around while balanced and threw her arms up, tracking the bullet's path. She pulled each trigger twice, sending Smith falling from the roof, his body hitting the ground with a thud.

_Strange,_ the analytical part of Lynx thought. _He didn't even try to dodge that._

A door to her left swung open and she turned around just in time to dodge a bullet from Smith's new body. She aimed and shot it in the head. Continuing her slow fall forward, she rolled and came up on her feet, pointing arms in a right angle towards the streets ahead of her. Smith appeared at both exits.

_What the hell is going on?_

Neo and Trinity stood on opposite sides of Voyd, looking over his shoulders.

"What the hell is going on?" asked Voyd, almost shouting.

Trinity wondered the very same thing. One Smith had killed Neo, who knew what _two _could do to poor Lynx?

As she had that thought, Lynx leaped onto a ladder running up the wall of a nearby building. She shot one of the Smiths and began scaling the ladder. 

As Lynx reached the halfway point, two more Smiths ran into the alley from the doorways below. As Lynx's hand touched the top rung, she felt a weight on it, and looked up into the barrel of a pistol.

"Greetings once again, Miss Hawkins," said a cold voice.

Neo looked at the screen in shock. _Four Smiths? What the _hell_ is going on? Lynx is gonna need some serious help getting out of this one._

The _Nebuchadnezzar _hurtled around a massive pillar, lines of destruction streaming from the rear guns. The pillar groaned as if wounded itself, and collapsed into the swarm of Sentinels, pushing a good number into the walls and crushing more under itself.

Sentinel 10-55A was a third generation Sentinel, smarter and better equipped then B or C generation Sentinels. It flew _over _the collapsing pillar and fired. Machines cannot feel, but it certainly had a sense of completion as its shot hit the rear cannons of the fleeing rebel craft, silencing them. 

10-55A switched to missile launchers and fired one. The projectile flew forward and struck the left back of the hovercraft. The ship took the hit gracelessly, spiraling around out of control, almost hitting the wall. The ship straightened back out, however. 10-55A could not admire, either, but his analytical programming told him the pilot of this hovercraft was ranked "Above Average," only a few steps below the pilot of Ship 011001 – The _ Logos._

Fallen Angel hit the pilot's yoke hard, slamming the ship into another tight spiral. Phoenix swore. "We've got no guns back there! And they hit the engines! We're losing speed, fuel, and power!"

"Holy shit, they couldn't have picked a better place to hit us! Their programming is getting better."

Phoenix thought. "Yeah, but human behavior is irrational. Listen, here's what we do."

Lynx cried out and tried to let go of the ladder with one hand, but the Agent's foot held it down firm. Lynx gazed into the unforgiving metal of the pistol, feeling fear for the first time since she had started training with Neo. All the training, everything she had worked for and aspired to was all about to come to naught.

The gunshot echoed over the roof.

It had all fallen apart.

10-55A was possessed with the most advanced human stratagem programs, and was utterly shocked when the hovercraft turned around and came head on, firing with its undamaged front guns. 10-56A and 10-54A had vanished from either side of 10-55A, and the hovercraft had swept through the machines like a stick through a swarm of bees, leaving broken metal in its wake.

As the ship barreled down the tunnel, 10-55A, now commander of Sentinel Scout Force 10110, called for a retreat. This new strategy had to be examined before they could dare to attack again. Hopefully, they would figure everything out before Sentinel Army Detachment 00001 reached Z10N.

10-55A and the few survivors began the long flight back to 01.

Fallen Angel looked at Phoenix with a new respect.

"I can't believe that dumbshit plan worked," he stammered. Phoenix smiled cockily. 

"I win the bet. Now you have to tell me how you got your name."

"Fine," Fallen Angel sighed. "Soon."

Pandora sat in her own private prison, composed from her own mind.

Her vision of hell was simple. She was trapped in the real world, aimlessly wandering the tunnels. Sentinels flew around her head, tiny ones, zapping her mind with their little lasers.

The pain was intense. Pandora screamed in her own little world, where no one heard her.

The Smith froze in place and toppled forward off the building. A familiar, rough hand grabbed Lynx's and pulled her up to the top of the building.

"Thanks." She gasped to Rabbit. Across the roof, Trinity sat on a bike, impatiently gunning the motor. 

"Let's go," she called.

"Where's Neo?" asked Lynx, perplexed. 

"He got held up," answered the first mate.

"Mister Anderson! Did you get my package?"

"Yes."

"Oh, good. Surprised to see me?"

"No."

"Then you're aware of it.".

"Of what?"

"Our…connection. I don't fully understand it myself, perhaps some part of you imprinted onto me, something overwritten or copied. It is at this point irrelevant. What matters is that whatever happened happened for a reason."

"And what reason is that?"

"Hurry up!" Trinity ordered. "Smith could return at any moment - "

The door to the roof swung open. A gun emerged, and a bullet emerged from that gun. It flew forward and struck the bike in the engine. Trinity had already reacted, years of training allowing her to start moving as the doorknob was turned. She was off the bike and five feet away when it exploded, lifting her into the air and letting her drop twenty feet away. She rolled and came to a stop by the edge of the roof, groaning.

Lynx swore and began firing. This Smith, however, dodged every bullet and sent a return shot at her. She leapt to the side, falling into Rabbit and sending them both to the floor. 

"I've changed, I'm unplugged. A new man, so to speak. Like you, _apparently _free," he continued.

"Congratulations," Neo said sarcastically.

"Thank you. But, as you well know, appearances can be deceiving."

Lynx pushed herself back into the air with one hand, letting go of one of her guns. The other she brought around and unloaded at the replica, making it pause to dodge. In that moment of hesitation, she struck.

Voyd looked at the screen in shock. "Holy shit, that's a lot of Smiths."

He switched views to Trinity and Lynx's situation. 

"Oh, shit, this is gonna be bad."

There was no sound first. Then it hit them. A rush of heat and sound, billowing up from beneath the building, exploding out in all directions. The shockwave lifted the four combatants off the building and throwing them into the air. Trinity, already injured, came down upon a landing of an adjacent office building with a thud, lapsing into unconsciousness. Rabbit and Smith landed on a building to the left, Smith upright, Rabbit stumbling and falling. Lynx rolled forward as the bomb exploded, tripping, accidentally propelling herself further into the air, and landing on the extreme edge of the same building as Trinity. She leapt to her feet, ready to rush over and help Rabbit.

Voyd held his breath. "Come on, get out of there."

The Smith lifted Rabbit high into the air and threw him against the wall. Rabbit groaned, his head rolling forward onto his chest as he slid to the ground. Smith cocked his foot and shot it into Rabbit's chin, lifting his head upward with a snapping sound. Rabbit yelled and fell forward. Grinning, Smith drew his pistol and emptied his clip into the stunned rebel.

Lynx watched from across the way. "No!" she yelled. She took a step forward. A revived Trinity grabbed her by the shoulder.

"There's nothing you can do for him. We must go, _now_. That's an order."

Lynx took one last look at the building across the way and flew into the building and up the stairs.

After a long, hard climb, they reached the top. Trinity and Lynx walked to the edge and looked around. They heard the hard line ringing somewhere. Lynx pinpointed the source of the ringing as an old shack across the way. As she took a step towards it, the door swung open to reveal Smith again.

"Shit, give us a break!" Lynx screamed in fury. Trinity tugged her backwards and drew her sidearm, pointing it at the Agent. She suddenly noticed a faint whistling sound from her left. Praying, she took a deep breath and jumped off the back of the building, pulling Lynx with her.

They fell fast, much faster then Trinity expected. They had reached the halfway point of the building when Trinity suddenly felt a pull as their fall stopped. Looking up, she smiled at Neo.

"Good timing."

Trinity sat in her room, staring at the wall.

He was gone.

That thought dominated her thinking. The pain was like a knife ripping through her, spilling tears instead of blood.

Rabbit was gone.

Her best friend – he had always been there for her.

Morpheus rubbed his forehead. He had a headache. He couldn't believe it. He was fighting for the survival of the very human race, and he had a _dammed headache!_

It was unbelievable.

Pandora lay stretched out on the table, breathing shallowly, life signs stable. Phoenix – who, ironically, considering his kamikaze attitude, was a medic – was examining her.

"She's definitely got something. Some life form I've never seen before is inside her. I don't think it's lethal, but it'll put her out for an indefinite amount of time."

"What happened?"

"As far as I can tell, she had a panic attack and fainted. She should be fine soon."


	6. Infrastructure

**Chapter Five: Infrastructure**

"Zion Main Control this is the _Nebuchadnezzar. _Can anyone here us?"

"Zion Main Control, can you read us?"

"Thi- Z- -ain Contr- -ver."

"Zion, you're breaking up!"

"-essage?"

"This is the _Nebuchadnezzar. _I don't know if you can understand us, but we need to get this out before our range expires. We've taken serious damage from a Sentinel attack, one crewmember is dead. The _Gnosis _and the _Hammer _are down, all killed except Pandora. We are going to try to end this was, and we could use any assistance. Over and out."

"Incoming transmission, captain!" called Sparks.

Niobe walked over to the monitor. "Put it up."

Commander Locke's face swam onto the screen. 

"Niobe," he greeted her calmly.

"Greetings, commander," Niobe returned.

Locke got straight down to business.

"We've received a broken transmission from the _ Neb_ requesting assistance. While I did not want to spare another ship to their aid, the Council ordered me too. Yours is the closest. I – we – need you to jack in to the Matrix, find Morpheus and his crew, and get them back to Zion. Fast."

"Can do, commander."

"Thank you, captain," Locke replied. "And Niobe?"

"Yes?" she asked.

"Good luck." 

The screen went black.

The phone rang.

Standing in a semi-circle around it were all the fighters that could be spared: Fallen Angel, Phoenix, Lynx, and, of course, Neo. Trinity had stayed behind to help Voyd watch the ship.

Neo picked up the receiver. "We're in."

Trinity's voice answered him. "Good luck. And Neo?"

"What?"

She seemed troubled, as if she was hiding something. 

"Nevermind. Watch your back."

Neo hung the phone up. He turned to the rebels. 

"Let's move out."

The building dwarfed the surrounding metropolis, casting a shadow on the other, less-important buildings. As Neo looked at it, the code making the structure up glowed bright green and began to shift quickly. He wondered what it all meant.

_"…In national news today, the Center for Homeland Security exploded inexplicably at noon. Security cameras from across the street caught a man of average height wearing a suit and glasses fleeing the crime scene. Officials identified the man as "A. Smith," calling him a rogue government agent. As a result of today's attack, security in all government buildings has been heightened._

_ In international news, Iraqi leader Saddam Hussein today called for a…"_

Only meters below the Mainframe Building, the system's worst enemies sat and plotted. 

"The door to the Source is here," Neo said, indicating a spot on the floor plans they had gotten from Voyd. "It's protected by a gauntlet of security men and droids, laser trip wires connected to a bomb, and numerous other traps we couldn't even begin to imagine. We need to get in here, but first, we need to get the power off."

He turned to Phoenix. 

"That's where you and Fallen Angel come in. Lynx and I will create a distraction while you two sneak in the back and cut the buildings power. The security office is located on the third floor. If you can get there, you can disable the droids and the bomb, and turn off the power.

"Once the power is off, you two get out. Lynx and I will head up to the floor 01, whatever that means. We'll find it. From there, it's just a skip, hop, and a jump to the Source. Got it?"

Everyone silently nodded.

"Good luck. And remember what Morpheus said to us earlier this week: tomorrow the war could be over. Isn't that worth fighting for? Isn't that worth dieing for?"

If machines could feel emotions, Agent Matthews would have been ecstatic. All was going according to plan.

The foolish rebels were walking right into his trap. They had met in the sewers below, and the Anomaly and Miss Hawkins were now coming to the front door, where Matthews had tripled the guard. The other two rebels were coming around the back, where Matthews himself waited. With his new upgrade, Matthews was confident he could handle two rebels.

Neo checked his guns one last time and stepped from the shadows of the alley into the main street. He walked through the moonlit road and towards the door of the Mainframe Building. He reached forward to push the door open, and a voice rang through the night.

"Neo, stop!"

Neo looked around. From across the street, he noticed the moonlight reflecting off a small spot. He stepped left in time to dodge the poorly fired bullet, and took off, running into the night. With one hand he grabbed Lynx and pulled her away from the door, and with the other he flipped open his cell phone.

"Phoenix, abort mission!" he yelled.

"What the fu - "

He hung up. As the two rebels dashed towards the alley, the door of the mainframe building flew open, SWAT programs pouring from the entrance. Neo and Lynx raced through the mouth of the alley, and the voice called to them. 

"Stay there!"

The SWAT kept advancing, firing as they came. Neo and Lynx evaded the shots, and as the nearest SWAT came within twenty feet of the pair, the ground exploded, flinging shrapnel high into the air. When the explosion and resulting dust cloud vanished, half the ground force was gone. The voice rang out again.

"Commence mop up."

From three separate directions fire poured onto the SWAT team. Neo and Lynx unloaded their own weapons onto the unfortunate programs. Within minutes, they were gone.

Hours later, they all sat in a room. With a small jolt, Neo realized it was the room where he had first met Morpheus.

_It's a site of beginning and end, _he thought to himself. He sat in the familiar red armchair, gazing out on the room from behind his normal sunglasses. To his left sat Lynx and Niobe. To his right were Phoenix and Fallen Angel. Across from him sat the remainder of the _Logos _crew, Myst and Ghost.

They all listened intently as Neo explained his plan. When he was done, Myst had only one question: 

"How, exactly, do you get to floor 01?"

A new voice emerged from behind them all.

"I can take you there."

The parking garage was deserted. Neo turned the door handle, revealing the programmer's hallway beyond. As Neo, Lynx, and their ally left through that door, Fallen Angel turned to the crew of the _Logos_.

"Good luck."

Niobe nodded to him. She opened the door of her van and climbed inside. She turned the key, and the noise of the engine shattered the perfect silence of the garage. Ghost walked past Phoenix, heading towards his own van. Myst turned to walk towards her vehicle, but then stopped and turned back to the pair from the _Neb._

"Phoenix…" she began, but then trailed off. A small tear glistened in the corner of her eye. Then she turned away and ran towards her van. Phoenix shrugged and walked out of the garage. Fallen Angel hurried after him.

"Team One, there is a vehicle approaching your location. Secure and report, over."

SWAT Program 10-55A stepped into the middle of the road, holding up its hand. The approaching van, with tinted windows, rolled to a stop in front of the barricade. The driver's side window rolled down and 10-55A glanced in.

A lightening-quick search of the database revealed the driver as Subject 15, Captain Niobe. This thought registered seconds before the Subject lifted a pistol from her lap and shot the program in its face.

"Team Two, be advised, Team One is down, repeat, Team One is down. Be alert for serious rebel activity. Over."

The van came roaring down the pathway, hitting the flimsy fence in front of the guardhouse and shooting past. Niobe jammed the steering wheel hard to the left, and the car shot around another turn. Niobe straightened out and saw the darkness give away directly in front of her. Jamming the gears, she opened her door and leapt out into the night.

The moving bomb sailed over the incline and began falling towards the city below. As Niobe hit the ground and rolled to a stop against a tree, a rush of heat and sound hit her. She curled into a ball and waited until it was all over.

"All units, be advised, serious rebel activity in the area. Grids G1 through G10: be ready for attacks on important sights with truck bombs. Team Six, report to grid G8 and secure power station. Team Two, report to grid G7 and secure power station. All other teams hold positions. Over."

Neo and Lynx entered the doors of the Mainframe Building's lobby. A bored-looking security program waved them over to the metal detectors. Neo shot him. As he collapsed to the ground, the other security men jumped up and opened fire. Neo held out his hands, and the bullets stopped in mid-flight.

"Holy shit," said one of the guards.

The pair of rebels opened fire. The three guards collapsed to the ground exactly five seconds later. From across the lobby, the elevators all dinged.

The second van roared past a checkpoint. One of the guards was quick enough to shoot at the van's retreating figure, but only managed to wing the rear bumper. He put the radio call into Central Protection Unit.

"Unidentified vehicle has passed checkpoint G7 without stopping, over."

"Thank you, G7," returned CPU. "We'll handle it."

The three elevator doors opened and SWAT programs poured from the doors. Lynx dropped her pistols and ran to the left, opening fire with an AK47. Her shots ripped into the first two men of Team One, dropping them to the floor. A third man opened fire with his weapon, and Lynx dove to the ground to avoid the salvo. She slid past the security counter and popped back up from behind the information desk, opening fire again and killing three more SWATS.

Neo pulled the pin from the grenade in his hand and slid it towards the SWATS. The sphere exploded, and screams filled the air. Neo fired his MP5 into the dust cloud as he ran forward. He jabbed a SWAT in the throat with his gun as he passed, and the SWAT collapsed the floor, gurgling and coughing blood. 

A beeping filled the _Nebuchadnezzar_. Voyd jumped, his concentration on the screen having been absolute. He keyed the intercom button. 

"Trinity, what's happening?"

Trinity had been torn between her loyalty to Morpheus and desire to watch over Neo. In the end, she had decided that Neo could take care of himself and stayed behind. She sat in the medical bay, watching over Pandora as Morpheus monitored the situation from the front.

"I don't know. I think she's waking up."

Phoenix pulled Fallen Angel back into the room as a group of SWAT team ran past them down the hallway. He poked his head back out and, seeing the hallway clear, leapt across to another door and pulled it open.

The guard behind the desk stood up.

"Hey, you're not supposed to be - "

Phoenix shot him. Fallen Angel slid into the computer console seat as Phoenix slid the door shut. Turning, he swore and shot out a camera.

"Hurry up, Fallen Angel, we're gonna have company real soon."

Fallen Angel ignored him. The computer screen read:

login

Fallen Angel typed:

run trojan.pif

The hard drive whirred and words began to fill the screen:

running trojan.pif

checking file…file clean

remote port?

Fallen Angel typed the address for the _ Nebuchadnezzar's _connection. Soon, Voyd's words joined the computer screen.

accept transmission?

y

run trojan.pif?

y

running: 1%

keep the port open for as long as possible

good luck

Phoenix called, "Any luck?"

Fallen Angel sighed in exasperation. 

"We just need to hold out a bit longer."

Phoenix thought for a moment. 

"Can you do anything to help us with that?"

Fallen Angel considered it. "Probably." He turned back to the screen.

The sound of bullets filled the air once again and another SWAT cried out before being silenced permanently. Neo dropped his weapon and drew his shotgun, blasting another SWAT in the stomach as he brought it to bear. He held it upside-down on his shoulder and shot a man behind him rising from the floor. Then he twirled it back down to standard position and blew the last man's chest in. 

"Freeze."

Ghost raised his hands. One of the SWATS walked forward to grab him when a roar caught their attention. Looking up, they spotted a van fly over the edge of the cliff and crash into the power relay station down the gorge. Everyone winced and ducked to avoid the explosion. Ghost grabbed the front man's weapon and jabbed the butt into the man's throat, pulling the trigger at the same time. The fire took out the other two men of the team. Ghost dropped the gun and ran.

The allyy entered the hallway and walked straight to the one undamaged elevator. He pressed the call button, opening the doors. Neo and Lynx clambered into the elevator behind him. The man pressed the button for the fiftieth floor. The doors closed with a ding, and the elevator began its long ascent.

running: 50%

"Almost done," said Fallen Angel nervously.

"It better hurry up, 'cause we're about to have company!"

These words were answered with a blast of fire coming in through the window. It smashed into the main overhead monitor, and the screen exploded, flinging shrapnel around. Fallen Angel typed rapidly.

turn inter-security on

locks?

y

glass?

y

password

override

call?

trojan.pif

accepted. security engaged

The door lock snapped shut and the bulletproof glass rose through the shattered window. "Good thinking," breathed Phoenix in relief.

"It's only for a short while," Fallen Angel told him. "They'll get to the generator and turn the security off with the power, and then restart it."

"Shit."

"Yeah."

"We better finish this first, then."

The screen read:

running: 62%

As the elevator passed the 48th floor, the guest hit the stop button. The elevator screeched to a halt between floors 49 and 50. The man removed a key from his pocket and opened the elevator doors. Beyond them lay a white hallway filled with green doors.

Myst checked her weapon one last time, and then climbed out through the sunroof of the car. As it hurtled over the edge, she leapt upwards. The van shot beneath her, crashing into the third and final relay station below. Myst landed in front of the station as it exploded behind her.

Security guards came running from all direction. Myst blocked the attack of the first one and kicked out sideways, sending him flying into another guard. The third one attacked with his stick, but she grabbed it and yanked it out of his hand, flipping it up and knocking him to the side with it. She flipped into the air, throwing the stick under her into the face of a running security guard. As her leap reached its zenith, her legs connected with the final guard.

Myst landed in a crouch beside the man she had just downed. He groaned, still living. Myst grabbed her dagger from her left boot, reached over, and slit his throat.

The power went out in the surrounding buildings, but in the Mainframe Building it stayed on. The building was already running on generator power as a result of the explosion in the lobby. Now only one barrier remained between death and victory.

running: 94%

Phoenix smiled. 

"We're gonna get it-"

The lights flickered. The room was plunged into darkness. Moments later, the lights came back on. The locks snapped open. The computer flickered off and then back on, beginning the slow process of rebooting.

"Shit!" yelled Phoenix. "There's not enough time left to do it again! What now?"

"Calm down," soothed Fallen Angel. "I have a plan."

Lynx stepped through the elevator doors, Neo following. They walked and opened each door systematically. They all led to useless places such as a park, or a sewer passage, or a mansion, except for the last door.

Te final door opened into a dark hallway.

"Here you are," said the Prophet. "Floor 01."

Neo stepped out of the hallway. "Thank you."

The Prophet nodded. "No problem." He turned to Lynx. 

"And I'll be seeing you again, soon." He turned around and left.

Neo looked at Lynx strangely. "What did that mean?"

She shrugged. "No idea."

"Neo!" called the Prophet. Neo looked back curiously. A shining object flew through the air. Neo automatically caught it and glanced down into his hand to see what it was: a bent spoon. Neo quickly looked back up, but the man was gone.

"Delta Bravo move forward."

"Cover me. Charge in place."

"Fall back!"

"Fire in the hole!"

The door to the security center exploded inward, knocked back by powerful bombs. The Delta Security team moved in, M16s at the ready, but lowered their guns at the sight they saw.

The room was empty.

"Go."

"Cover me."

Fallen Angel popped up from cover and began running full-out, pumping his legs as fast as he could. A sniper broke cover to fire at him, and Phoenix shot the man in the head. Fallen Angel dashed around a corner and with one hand armed the timer.

He skidded the bomb across the floor in front of him, turned around, and ran faster then he ever had before. Behind him, the timer reached zero, and the bomb exploded. The explosive force lifted Fallen Angel off the ground and blew him onto Phoenix, tumbling them both to the floor.

Phoenix looked up into Fallen Angel's eyes. 

"Get off me."

Fallen Angel got up and then helped his partner to his feet.

Neo walked forward to the last door in the hallway, Lynx behind him on the left. He instinctively knew this was the door. The one door he had fought to reach for what seemed like forever. He knew others had been fighting for him to reach it for a lifetime. He put his hand on the doorknob.

Myst climbed out of the depression. Flipping her cell phone open, she called Niobe.

"Captain, it's me."

"Myst. Ghost is dead."

"No!"

"I'm under pursuit, can't talk long. Get to the rendezvous point. As quick as-"

Myst's captain's voice broke off and the sound of gunfire filled the phone. Then she heard tires squealing, a woman scream, and an explosion.

Ghost looked up as the Firebird pulled to a stop in front of him. He slid into the passenger's side door. "Captain."

She nodded her greetings. Ghost wondered why she was so serious at the moment, and then she told him.

"Myst is dead."

Ghost was silent for a moment. Myst was barely twenty. _This war is gobbling up children like a starved dragon._

Ghost sighed. Niobe pressed down on the ignition and the car leapt forward into the night.

Neo twisted his hand and the door opened. The world suddenly became an explosion of light, dimmed only slightly by the sunglasses Neo always wore. The light receded and left Neo standing – no, floating – in a sea of stars. He waded forward and grabbed one, holding on tight. There was a rush of heat and power, and awareness faded.

Neo was left standing in a white hemisphere of a room. In front of him sat a man on a chair. The man was tall, white-haired, and wore a perfectly clean white suit.

"Who are you?" asked Neo.

"I am the Architect," answered the man. "I created the Matrix."


	7. Revelations

**

Part Two: Reign of Chaos

**

_"But as you well know, appearances can be deceiving, which brings me back to the reason why we're here. We're not here because we're free; we're here because we're not free. There's no escaping reason, no denying purpose - because as we both know, without purpose, we would not exist."_****

* * *

**Chapter One: Revelations**

Trial by fire.

Such a cliché, such a trite phrase, Myst had always thought. But she knew she was now facing hers.

The words pounded in her head as she jogged along the empty streets.

_Ghost is dead, Ghost is dead, Ghost is dead…_

Like gunfire they kept pounding her as she ran along. Her side ached and her lungs burned. She was gasping for air. She stumbled, catching herself on a bench. Then she dropped to all fours and vomited over the sidewalk.

_Why didn't I take the blue pill?_

They had all had their moments of doubt. She knew it. But even a momentary betrayal of purpose was a betrayal of Ghost's memory. She pulled herself up and continued on, faster then before.

"Lynx."

The voice was not calm and commanding, like that of an Agent. The voice was full of fire and rage, barely restrained anger and violence. It also spoke her true name, which got her attention quicker then the first face.

She turned around, her black cloak billowing out behind her, guns coming out form their holsters and pointing forward. Unthinkingly, she squeezed off two shots from each weapon. The bullets traveled forward, and then suddenly exploded as if they had hit a wall.

Standing at the end of the hallway was what could only be a demon from hell. His hair was flaming orange, spread down his neck. Massive red wings spread out behind him, taking up almost the entire hallway. Fingernails were stretched into long, razor sharp claws. And black sunglasses barely concealed the red glow of the eye beyond them.

"Lynx," the apparition said again. 

"I'm afraid I haven't had the pleasure," the rebel replied sarcastically, keeping a tight grip on her guns. 

The demon seemed almost hurt. 

"You don't remember me, Hawkins?"

"Can't say that I do. I tend to remember the ugly ones," Lynx replied scathingly.

The man frowned. "That was uncalled for."

"Are you going to move," Lynx asked, fed up with the idle chat, "or do I have to make you?"

The man grinned. He held out his hand and a fireball burst into being.

"I'd love to see you try."

"You have many questions," the Architect told Neo, "and while the process has altered your consciousness, you remain irrevocably human. Ergo some of my answers you will understand and some of them you will not. Concordantly, while your first question may be the most pertinent, you may or may not realize it is also the most irrelevant."

"Why am I here?" asked Neo.

The world was fire.

The fire surrounded Fallen Angel. It licked his hair and heels, singing his cloak and face. He ran as fast as he could, trying to outrun the flame. Beside him ran Phoenix, seemingly one with the flame, barely minding the heat at all. 

Fallen Angel leapt up from the ground, grabbing the bottom rung of a partially destroyed ladder. He pulled himself up the rungs, the climb shooting pain through him every time he touched his burnt palms to the rungs.

He reached the top and climbed to his feet. Reaching down, he pulled Phoenix onto the landing. They surveyed the surrounding landscape.

"There."

Fallen Angel followed Phoenix's finger to see a military van sitting unguarded down below. Fallen Angel nodded his silent agreement and began the long, painful climb down.

Myst stumbled along the dark alleyway, her shadow stretched out on the wall. Her blond hair, usually perfectly clean, was now smattered with blood and dirt. There was blood all over her right hand, and all over the dagger stuck into her left boot.

Myst swayed as she walked, barely able to keep her eyes open. Every other step sent pain shooting up Myst's left leg. Myst suddenly overstepped and fell forward, her face hitting the ground. Darkness overtook her.

Lynx ran to the left and the fireball flew past her. She blasted away at the apparition, but her bullets had the same effect as they did on any Agent – none. Lynx headed into a large conference room and jumped up on the table. Lucifer entered the room, his huge wings barely fitting through the doorway. He opened his mouth and fire streamed out, licking the edges of the table. Lynx jumped backwards, landing on her feet. Turning sideways, she kicked out the window and jumped out, falling – 

- two feet to the ground with a hard thud.

_The Matrix sure is some weird shit, _she thought to herself as she scrambled upward and began running. From the window behind, Lucifer roared and smashed through the wall.

Neo suddenly had a moment of revelation. "The problem is choice."

"The first Matrix I designed was quite naturally perfect; it was a work of art - flawless, sublime. A triumph equaled only by its monumental failure. The inevitability of its doom is apparent to me now as a consequence of the imperfection inherent in every human being. Thus, I redesigned it based on your history to more accurately reflect the varying grotesqueries of your nature. However, I was again frustrated by failure. I have since come to understand that the answer eluded me because it required a lesser mind, or perhaps a mind less bound by the parameters of perfection. Thus the answer was stumbled upon by another - an intuitive program, initially created to investigate certain aspects of the human psyche. If I am the father of the matrix, she would undoubtedly be its mother."

"The Oracle," said Neo.

"Please," said the Architect dismissively. 

The driver's side door and passenger door slammed shut. Fallen Angel pressed the pedal down and drove off into the night. After a few minutes had passed in silence, he looked over at Phoenix.

"Talk."

Phoenix sighed and began his story.

_"Okay crew," Niobe said. "We've got a mission."_

_ "Finally," Phoenix said, drawing some chuckles from the other members of the _Logos's _crew._

_ "Quiet," Niobe told him impatiently. "We need to reach a site inside the Matrix called "Club Hell." Waiting there is an informant who will pass us information about the Matrix's inner workings."_

_ "Sounds like a trap to me," Sparks said. "You guys are crazy to even _think _about going-"_

_ "Sparks, shut up."_

_ "Sure, why not?"_

_ They had all lined up and jacked in, Niobe, Ghost, Phoenix, Myst, Hawk, and Shade. Some they found themselves standing on the road across from a building, an S&M club called "Club Hell." Everyone looked at each other, wondering _"Now what?" _Shrugging Phoenix started across the road._

_"Phoenix, wait!" Niobe yelled. Phoenix ignored her. "Get back here, dammit!" she yelled._

_Phoenix reached the door of Club Hell and flung it open. An ear-splitting wail filled the streets. The occupants of the club vanished, and guns lowered from the ceiling, opening fire on the rebels. Phoenix dived to the left and made it to cover. The others were less fortunate then him._

_ From the building behind them emerged ten troops. Niobe yelled "Fire!" and suited action to words, gunning two down. The wounded men, however, immediately got back up. _

_ "What the hell?" screamed Shade, opening up with an M16. The attackers charged forward, one barreling into Myst and sending her flying. Ghost grabbed one by the wrist and flipped him over a shoulder, knocking him out cold._

_ Phoenix leapt back to his feet, running to join battle. As he ran, he loosened a grenade from his belt and sent it sliding along the ground. It reached the main attack group, exploding in their midst and ripping most of them to shreds._

_ Then _they _came. There were three of them. Their leader was a tall man, whose black hair fell down to his shoulders. He wore jet-black sunglasses and a dark cloak. His name, they later learned, was Drake._

_ He was flanked by two albino men wearing white suits. Each member of the trio had a gun out and was pointing it at one of the members of the _Logos. 

_"Greetings, Niobe," Drake said. "Nice that you could join us."_

_ Niobe remained impassive. "I don't believe I've had the pleasure."_

_ "You haven't. But that was _my _club you were about to invade. And we don't take kindly to invaders."_

_ Phoenix readied himself. There were only three of them, they could take them. He glanced over at Niobe, and she shook her head. At the same moment, Myst raised her head, saw the trio, and groaned. Drake shifted his view for a second, and in that second Phoenix struck. He kicked out at Drake's knee, sending the man to the floor. Hawk raised his gun again and fired at one of the albinos. The albino suddenly became incorporeal, the bullet flying through without harming him. Hawk stared._

_ The albino returned to his natural state. _

_ "We wouldn't do that if we were you," he said calmly. Then the Twins struck._

_ They moved together flawlessly, accenting each other perfectly. One charged forward at Hawk, who braced himself for hand-to-hand. As One reached the rebel, he phased again, and Two fired. A bullet hole appeared in Hawk's head, and the rebel collapsed forward._

_Drake reached up and pulled Phoenix to the floor. Phoenix cried out and pulled the trigger, the bullet flying wildly and hitting Shade in the arm. He screamed in pain. One grabbed Shade's wound and pressed down on it, forcing the rebel to the floor. Niobe ran forward but the Twins drew guns at the exact same moment, One pointing at Shade, Two pointing his at Ghost, and Drake holding Phoenix in a headlock._

_ "Freeze," One ordered. "Step away."_

_ Niobe backed up slightly. Two nodded. _

_ "Stay there," he ordered in a raspy voice. Drake stood up, rubbing his injured knee._

_ Two indicated the injured leader. _

_ "We owe you for that."_

_ Drake snapped his fingers. Minions appeared from the nearby alleyways and building mouths. Drake motioned towards Niobe, Ghost, and Phoenix. _

_ "Escort them away," he ordered. Turning to Niobe, he said, "Your informant has been killed. Leave this place and do not return."_

_ Drake disappeared into the shadows. The Twins backed away slowly, keeping their guns trained on the group. As they faded away, One pulled the trigger again. Shade fell._

_ When they finally reached safety, Niobe turned to Phoenix and said the two simple words that would haunt him for the rest of his life._

_"Fuck you."_

_ And she had walked away._

Myst finally reached the rendezvous point. She entered the warehouse cautiously, gun drawn. She poked her head around the corner, checking to see if the coast was clear. Then, straightening, she walked to the entry and exit point, picking up the phone and dialing the_ Logos's _ number.

It rang three times. No answer. That was strange. Sparks was always very prompt in answering. What could be happening in the ship?

Unbeknownst to Myst, Sparks was dead. His throat had been cut, and blood had splattered across the keyboard and monitor screens of the Matrix. His face was locked into what had been his final expression: one of extreme annoyance.

The other members of the ship slept on in the Matrix chairs. The ship's crew was, of course, unaware of Spark's death, just as they were unaware of the intruder now exiting their ship.

"You are here because Zion is about to be destroyed - its every living inhabitant terminated, its entire existence eradicated," confirmed the Architect.

"Bullshit!" Neo shouted firmly, his mind echoing the sentiment.

"Denial is the most predictable of all human responses, but rest assured, this will be the sixth time we have destroyed it, and we have become exceedingly efficient at it."

As Neo debated with the old program, the traitor somehow saw the conversation in his dreams. He had "watched" from the beginning, with growing horror, realizing the lies the human race had been told. And slowly, inevitably, he gave in and believed.

The traitor awoke. And, upon waking, he began to outline a plan to get him back into the Matrix.

Lynx fired over her shoulder as she ran, the bullets still useless. She dropped her empty pistols and ran faster, turning a corner, with her cloak billowing out behind her. She jumped slightly, kicked off a wall, and hit Lucifer in the head as he rounded the corner after her. He went flying to the ground.

Rising, he wiped the blood from his mouth with the back of his hand. "That was a mistake, girl," he snarled. Lynx cartwheeled gracefully, coming up just a few feet short of Lucifer, ready to fight.

"I think not."

Still no answer. Myst's throat was now dry from worrying. Her suit was covered in blood from her wound, and her vision was slowly dimming. She was losing her grip on reality. As she continued to listen to ringing, the phone slowly slipped from her hands. 

_Why doesn't he answer? _Myst thought. And with that thought echoing in her mind, she slipped into darkness.

"Which brings us at last to the moment of truth, wherein the fundamental flaw is ultimately expressed, and the anomaly revealed as both beginning and end. There are two doors. The door to your right leads to the Source, and the salvation of Zion. The door to your left leads back to the Matrix, to her and to the end of your species. As you adequately put, the problem is choice. But we already know what you are going to do, don't we? Already, I can see the chain reaction - the chemical precursors that signal the onset of an emotion, designed specifically to overwhelm logic and reason - an emotion that is already blinding you from the simple and obvious truth. She – everyone - is going to die, and there is nothing you can do to stop it."

Lynx exploded into a whirlwind of motion, kicking out at Lucifer with both feet. Lucifer stretched back, evading Lynx's blows, and slashed his hand upward across her stomach, ripping holes in her fabric, and in her skin.

Lynx gasped from the blow and dropped to the floor. It hurt more then it should. Lucifer smiled.

"Poison, my dear. Very painful, very fast-acting, no antidote. The bleeding won't stop either."

Lucifer leaned forward, mouth close to her ear, and whispered. "You are dead."

Lynx growled to herself. "No!" She shot her fist upward, hitting Lucifer in the face. He staggered backwards, and Lynx shot to her feet. Lucifer regained his balance and glared at the rebel.

She stared back confidently. "I may be dead, but so are you."

Lucifer slowly smiled, shaking his head. "So naïve, little Lynx." He suddenly thrust his hands forward and a wave of fire streamed from his palms. Lynx screamed as the flames ate at her flesh. She took a step forward and fell, the fire going out as she hit the ground.

Lucifer knelt down beside her. "Too bad it had to end this way, my dear." He lifted her head up and kissed her. His lips were like fire, and when he withdrew, Lynx knew her lips had been burnt to blackness.

The next sound was Lucifer heading away. Lynx pulled herself up and continued onward.

Neo started towards the door leading back to the Matrix. The Architect stopped him with a thought.

"Hope. It is the quintessential human delusion, simultaneously the source of your greatest strength and your greatest weakness."

Neo glanced at him coldly. "If I were you, I would hope we don't meet again."

The Architect waved his hand. "We won't."

Neo went through the door.

Lynx wandered one of the streets of the Matrix. She had no idea where she was. Every step was like Lucifer's claws ripping through her flesh again. Her lower body was covered in blood, her hair burnt, her skin singed, and her clothes in tatters. She wouldn't even be able to fight off a human in her current condition.

The car pulled to a stop in front of a large, ornate mansion. Ghost looked around in confusion. _This certainly isn't the extraction point…_

"Niobe?" he asked questioningly. She stared forward. Ghost glanced behind him. Suddenly, he felt a biting pain in his neck and he swiftly fell into unconsciousness.

The pain was gone now. Lynx took another step and fell forward, hitting her head on the ground. Slowly, but gratefully, she let the darkness overtake her.


	8. Betrayal

**Chapter Two: Betrayal**

The world swam back into focus. Ghost felt a throbbing pain in his head. His eyes stared up at a high ceiling made from old stone. Ghost reached out and climbed to his feet. He turned around and spotted a door. He ran to it, grabbing the knob and trying to force it open. The door refused to budge.

Their was suddenly a whirring sound and the Twins stepped through the wall.

"No one leaves," One said.

"Without _his _permission," Two finished.

The Twins grabbed Ghost by his arms and dragged him back down. The door to the makeshift cell swung open, and in walked the Merovingian.

"Greetings, Ghost. Glad you could join us."

"The pleasure's all yours."

"Come now, Ghost, is that a way to greet an old friend?"

"The number you have dialed has been disconnected. Please hang up and try again. The following tones are for the hearing impaired."

Myst waved the words away with her hand, only wanting to continue. A blaring ringing tone shot through her head, feeling like a multiple kicking against her wounded brow. Myst grabbed the phone and slammed it back down onto the receiver. She got to her feet.

Myst saw the blood on her clothes had dried and her wound had clotted. She glanced at the clock hanging on the wall.

_I've been out for thirty minutes? Impossible!_

She walked to another room and grabbed some aspirin from the emergency medical kit. She downed the pills with a glass of water and washed. She walked back to the armory, selected two handguns and a shotgun, and left the safehouse.

Beeping woke Lynx too. But it was a different sort of beeping. She wearily glanced around her, taking in the machinery and other surroundings. She was in a hospital.

A man near the door was sleeping in a wooden chair. Lynx called out to him. He woke up, took in Lynx, and yelled outside, "She's awake."

Two men rushed in. One was a doctor, and he began checking Lynx's vitals. When he was done, he looked up.

"She'll be fine." He turned to Lynx. "You're very lucky. The injuries you've sustained would've killed most people." The doctor left the room.

The second man was tall, and he wore a suit and glasses. 

"Well, Miss Hawkins, it seems one of our wayward children has returned home. Welcome back," he said. Lynx looked back blankly. The man laughed and left the room.

It all came back to Lynx in a rush.

_Wailing lights. Bright. Keep them away. Laughter. Screams. Laughter. A man. That man. A room. This room. Pain. It hurts. Men. Rebels. Neo. Source! MATRIX!_

She screamed. The man near the door looked at her and backed out. Lynx looked to her left, spotting a card on her bed. It read:

"Secure Facility for the Criminally Insane."

"That's an interesting tale," Fallen Angel said tactfully. Phoenix was silent, brooding. After a few minutes of silence, he spoke, his voice filling the car.

"How far are we from the nearest hard line?"

"Miles yet," Fallen Angel answered back.

"Good. You still haven't told me your story."

Fallen Angel sighed and began his tale of the day he remembered as "The Fall."

_It was one of those perfect days. The sky was blue, the breeze was perfect, and the sun was bright._

_ They had come to ruin that day for the humans._

_ Angel, Tsunami, and Raven stopped near the corner of the building. Angel kept a lookout with Tsunami while Raven placed a charge on the corner of the building. The three had started away at a brisk walk when the dreaded shifting sound came from their left. They broke cover, scattering in all three directions._

_ Raven took off down the alley. Angel ran left, pushing a businessman talking on a cell phone into a woman carrying a child. The man shouted "Hey!" after him, but Angel could care less. Tsunami dashed right, ducking around a woman with a stroller._

_ From across the street the Agent drew his gun. People screamed and ran for cover. The Agent popped off a shot at Tsunami, but his aim was bad and he hit a bystander. Angel drew his gun and fired at the Agent three times. The Agent dodged every shot._

_ Raven appeared from a side street and fired twice more. The Agent dodged left and fired his own gun, the shot catching Raven and throwing him back into the very building they'd come to destroy._

_ "Raven!" Tsunami screamed._

_ The rebel weakly lifted his weapon and emptied the clip at the Agent. He hit nothing but air. The Agent took his time, aiming precisely. There was a loud bang, and Raven slumped to the floor._

_ Tsunami backed away, firing pointlessly. She turned, dropped her weapon, and ran. The Agent chased after her, shoving a man out of his way and into a building. Angel ran over to Raven._

_ "Raven?" he asked tentatively. Raven groaned. He reached into his pocket and withdrew the detonator, pressing it into Angel's hand._

_ "Go," he whispered, and died._

_ Angel got up and ran after where the Agent had disappeared. He fired his weapon until it was empty, and then dropped it. He ran towards the Agent and jumped, landing a flying kick on his back. The Agent stumbled forward. Tsunami dashed past the program, grabbing a ladder hanging from the fire escape of a building and pulled herself up it, disappearing into the building._

_ The Agent whirled on Angel and threw him to the mouth of the alley. Picking himself up, Angel ran out into the crowd. The whirring of sirens heralded the arrival of the police. Men poured from squad cars, pointing their guns at Angel._

_ "Freeze!"_

_ The Agent came out of the alley. The policemen shifted their views for a second, and Angel took off. He flew through the street and into an apartment building._

_ Tsunami appeared on the other side of the street. She shot two policemen and disappeared._

_ Angel reached the roof. He opened the door and looked into the barrel of the Agent's pistol. He saw Tsunami vanish into the target building._

_ He pressed the trigger._

_ The building exploded. The Agent turned, and Angel threw him to the ground, running across the roof. He jumped across a gap between to buildings, climbed down the stairs, answered the phone, and vanished from the Matrix._

"You can not keep him here, my love," argued Persephone.

"I must," the Merovingian said. "It is essential to the plan."

"I agree with Persephone," Vlad said. "Keeping that dangerous rebel here is a mistake."

"We must protest your lack of faith," the Twins said. "We can handle the rebel."

"You heard them. They can handle it. And surely, Vlad, your forces are enough to contain any damage and repel any attackers," the Merovingian finalized.

"Of course they are, but my motto is anything that can go wrong, will."

"Fine, but remember, my love, I will be on hand to clean it up after it blows up in your face again," said Persephone, ending the conversation.

The door swung back open. The Merovingian left the meeting room walking at a rapid pace, the Twins struggling to keep up. Persephone walked from the room at a slower, more dignified pace. Last of all left Vlad, his pale face twisted into an expression of extreme thought.

Vlad walked right through a hanging tapestry and up a flight of stairs. He had entered the area of the dwelling that the Merovingian referred to as the "lair." Here lived the lesser Exiles, the Merovingian's minions. Vlad walked between to men fighting over a scrap of meat, snapping their long teeth at each other and yelling, almost barking.

He swept aside another tapestry and entered the Cave. He walked across the bridge leading over the hot springs where his minions bathed. Crossing into his own room, he summoned his lieutenant, Fang, to his side with a thought. The eager, freshly-bitten vampire, a former rebel named "Tyger," appeared instantly inside the room, stepping out of the shadows in the corner.

"Yes, master?" he hissed in question.

Vlad waved him over to a map of the Chateau. "Let us plan our defense for the Chateau. I have a feeling we will need to use it soon."

Myst reached the computer café just as it was closing. The owner opened the doors again at the sight of her gun and was glad to give Myst hours of free computer time.

"And an ice coffee," Myst told her. "Make it fast."

Myst logged on under the _Logos _account and quickly took remote control of the ship.

access remote camera

password?

sparksisdaman

sector?

core

The camera view popped up on Myst's screen. She jumped in shock as the camera showed Sparks, his throat cut, blood all over the monitors. She swore, loud. The owner looked at her in fear and hurried over with the coffee.

_Shit, shit, shit, _thought Myst. Her analytical mind took over, numbing the pain. Quickly, she typed:

run hardline.exe

dial?

Myst quickly searched the database for the nearest hard line.

0011005663245

dialing…

Myst stood up and ran out the door, leaving her ice coffee.

Lynx broke her chains off the bed, stood up, and hit the guard to the side. The man flew into the wall and collapsed forward. Lynx kicked her door open. All activity in the hallway halted. Three Agents turned around and stared at Lynx.

"Shit," she said mildly. One of the Agents snorted in laughter. The other two raised their guns.

Lynx ran.

Myst ran through the closed shopping center silently. She could faintly hear a phone ringing. She ducked under the half-closed gate of an electronics store and ran down the aisle. She vaulted over the desk and grabbed the ringing handset. She pressed it to her ear and disappeared from the store. The handset fell to the floor, an unexplained surprise for the shopkeeper who would open the store the next morning.

Lynx leapt over a counter, kicking the attendant to the side. The three Agents chased after her, firing their guns. The bullets whizzed past Lynx's head, hitting the wall and ceiling around her. She turned left, dashing through a pair of automatic doors. One of the Agents came from around the corner, lifting his gun up and tracking her path. 

He fired. Time seemed to slow. The bullet streaked towards Lynx. She saw the path but was unable to stop. She barreled into the shot.

Time returned to its normal flow. Lynx staggered backwards and fell to the floor. The Agent ran and kicked her, sending her flying into the parking lot. A car screeched as it hit the brakes to avoid her. Lynx got to her hands and knees. She heard a scream, gunfire, and the thud of a body hitting the floor. She fearfully looked up…

Fallen Angel hit the brakes and the van screeched to a stop in front of a bank. They could here the phone ringing inside. Phoenix kicked the window, shattering the glass. Fallen Angel followed him into the bank.

They tracked the location of the phone to a secretary's desk in the back. Fallen Angel lifted the receiver to his ear and vanished. Phoenix replaced the phone and waited for the ring, then followed Fallen Angel from the Matrix.

…and saw the palm in front of her. She grabbed it, and Trinity pulled Lynx to her feet. Lynx looked around. Morpheus had taken on two Agents, firing his two MPXs in their direction, filling the air with lead. Pandora had hacked herself a sword, and as Lynx watched, she sliced one of the Agents into bits. Trinity shoved Lynx back towards the hospital. 

"Go!" she ordered. "Find the hard line!" 

Lynx ran back into the hospital, glancing back to see Trinity push Pandora after her. Morpheus backed up slowly, firing as he went. Trinity also had her gun out, and was shooting with great accuracy. One of the Agents, dodging Morpheus's shots, got hit in the leg by Trinity and went down. The final Agent broke cover and ran at the two, diving and corkscrewing through the air. The fighters dropped their guns and ran.

Lynx got into the hospital and ran to the front desk. She slammed the attendant into the ground as he reached to answer the phone. She picked it up herself and vanished from the Matrix.

Pandora replaced the phone and waited. It rang. She reached for it. An Agent rounded the corner, pistol drawn. Pandora picked up the phone. The Agent fired. She pressed it to her ear.

The bullet hit her in the head. Pandora fell. Trinity ran into the hall, spotted the Agent, and turned around. "Go back!" she yelled to her captain, but the other two Agents were approaching from that direction.

They were trapped.

Voyd watched the screen. "Come on," he said anxiously. "Run!"

Myst opened her eyes onboard the _Logos._ She reached back and pulled the spike from her head, letting out a breath as she did so. She got up from the chair and looked around. Niobe was still slumbering in her chair, and past her…

_Ghost! Niobe said he was dead!_

Myst ran to the monitor and wiped the blood off. She quickly found Niobe inside the Agent. She was sitting in a comfortable chair, sipping tea, and chatting with a man Myst recognized only too well.

_Drake!_

Myst found Ghost. He lay unconscious inside a room, chained to the wall. Niobe had lied. She was a traitor.

Myst walked away from the monitor. She traveled to the galley, picked up a knife, and walked back to the Core. She walked to Niobe's chair and raised the weapon above her comatose form.

Myst dropped the knife. It clattered on the floor.

"I can't do it," she sobbed to herself.

Trinity jumped into the air and kicked off a wall, shooting back at the Agent and knocking him over. Morpheus dove for the phone and hung it up. It rang instantly. 

"Go!" Trinity yelled. Morpheus picked up the receiver and vanished. Trinity flipped over the counter, drawing her backup pistol, and hung the phone back up. She fired at the Agents, and they dove for cover. Then she gratefully lifted the receiver.

Morpheus stared at the floor. 

"I don't understand. The war should be over."

Neo nodded his agreement. "All I know is that unless we do something within twenty-four hours, it will be."

"But what about the Prophecy?" Trinity asked.

"The Prophecy was a lie. It was all just another system of control."

"What now?" asked Lynx.

"I don't know," Neo said.

They all stood in silence for a moment. Then Voyd spoke up.

"There is one thing we could do."

Morpheus looked at him expectantly. Voyd continued. 

"Before he died, Rabbit developed a program specifically designed to kill Agents and other programs of the system. If we could tie it into the Source, or the Mainframe, or some other - "

Morpheus nodded. "Call the _Logos._ Let's do it."


	9. Upload

**Chapter Three: Upload**

"_Nebuchadnezzar, _this is the _Logos. _ Can anybody hear me?"

"Myst?"

"Trinity? Thank God!"  
"What?"

"Trinity! Niobe – "

"What?"

"She – "

"What?"

"She – "

"Get a hold of yourself, Myst!"

"Ghost is caught!"

"How?"

"Niobe…traitor…"

"What?"

"She…Drake…Ghost…jail…"

"Holy shit."

Voyd typed away at the console furiously. They had little time. He quickly sliced a way into the Matrix for the elite of the _ Neb._ He turned to the captain.

"It's messy, Morpheus, but it'll do it. Get in quick, because the window closes in one hour. If you're not through the rabbit hole by then, the Mainframe will close and you'll be locked out."

Morpheus nodded his understanding. "Alright, jack us in."

The rabbit hole was an old, run-down house in an abandoned section of Chinatown. Morpheus walked point, ahead of the other two, eyes open to any threat. In the rear, Neo and Trinity walked side by side, silently giving each other strength for what lay ahead.

Morpheus reached for the door of the shack. The door slowly creaked open, a green light pouring out into the street. Pedestrians turned to glance at the trio queerly. Neo stepped forward, crossing the threshold. He turned and glanced back at Trinity. Then Neo's body dissolved into a flash of green code and zipped into the shack. Green tendrils of light snaked out and hit Morpheus and Trinity too, and they were sucked down the rabbit hole.

The three floated in the eye of the storm, unaware of self, unaware of the other two, but all connected as one.

_What now? _came a thought from the consciousness. It carried with it a sensation of a minor cold, like ice, scraping up against a brain.

**I don't know.** The second "voice" was calm, cool, and firm. It demanded respect.

**_Let's go,_** said the third voice. It was a mix of the other two, shaped and formed by its friends. The other two voices heeded to its call, and the three floated down the vortex. 

_"Good morning, Trinity. Cookie?"_

_ "No thank you."_

_ The Oracle seemed unsurprised. She pulled a chair out from the table for Trinity, who sat down gratefully. _

_ "So why are you here, Trinity?"_

_ "Morpheus says all the recruits come here."_

_ "But why are _you _here?"_

_ Trinity thought for a moment. "To find the truth."_

_ "Good answer," said the Oracle, sitting down and rolling a Coke to Trinity. Trinity picked it up and popped the top, taking a deep drink._

_ "You're not the One."_

_ The Oracle's proclamation did not surprise Trinity. Deep inside, she had known it wasn't her. But was hope such a bad thing?_

_ "But you will know him."_

_ Trinity looked up in interest, paying closer attention as the Oracle continued._

_ "Your life will be filled with troubles, pain, and loss, Trinity. Many of your friends will die in one disaster that you will not be able to prevent. You will be devastated, but will find healing in the arms of your new love…and that man will be the One."_

_ Trinity shifted uncomfortably, but her eyes showed nothing from behind the glasses. The Oracle stood back up, throwing her Coke can basketball-style towards the trash can and missing._

_ "Shoot," she said, walking over to pick it up._

_ "Didn't you already know it was going to miss?" Trinity asked, slightly sarcastically._

_ "Of course. Wouldn't be much of an Oracle if I didn't."_

_ "Then why bother?"_

_ "Even if all seems black, you've got to keep trying and hoping. Because that's what's important over all else, the trying and the hoping."_

_ The Oracle led Trinity to the door._

_ "A suggestion, Trinity. Get some rest tonight. You'll need the energy for tomorrow."_

_What is this place?_

**I think…**

** _This is the Source._**

****_What?_

**This is the Source.**

_"Morpheus," said the old woman, greeting him at the door. Morpheus shook her hand and was lead into the kitchen, where he was greeted by another woman._

_ "I'm the Oracle," she told him. "Not quite what you expected, huh?"_

_ "No," Morpheus admitted. He sat down on a chair by the doorway, feeling slightly awkward._

_ The Oracle handed him a cookie. As he was eating it, she pulled up a chair and sat down next to him._

_ "You're not the One."_

_ Morpheus nodded slowly. He'd known the truth deep inside of him._

_ "Locke will be disappointed," Morpheus said mildly. "Access really had him believing in me."_

_ "He'll be fine, considering he has a promotion coming up in a week. He is going to replace Scythe."_

_ "Huh?"_

_ "Scythe is sick and tired of fighting. He's retiring. You and Locke will not get along, but Locke is a smart man. You'll receive your own ship from him. And you will find the One."_

_ Morpheus paused a second to absorb the information. He started to speak, but the Oracle interrupted him._

_ "And your crew will make all the difference in the war. But I have to tell you, Morpheus – and it hurts me to do so – that you won't be there to share the end with them."_

_ Morpheus let that wash over him._

_ The Oracle got up and showed him to the door. He stood outside, and the Oracle shook his hand and gave him another cookie._

_ "Goodbye for now," she said. "Good luck."_

A call came from the Source itself, a pounding at the head. The call was loud and persistent; it jarred the thoughts, and broke the entity's concentration.

Another voice emerged from the Source, one tinged with bitterness and pain.

"Well," it thought. "I never thought I'd see you all again."

_All?_

The Source's call was pounding in their heads, telling them to ignore self and slip back into the proverbial primordial soup. The Source was claiming its wayward children.

**Trin-**

_What?_

**What?**

The fourth voice laughed at them. "Neo, Trinity, Morpheus."

**_Huh?_**

The first voice had a thought rise to its section of the single mind. It was an image of a human – a man. The man's arms enfolded the voice's self and whispered, **_I'll never leave you._**

****

**_ "_**_Neo, please, listen to me. I promised to tell you the rest. The Oracle, she told me that I'd fall in love and that man, the man I loved would be the One. You see? You can't be dead, Neo, you can't be because I love you. You hear me? I love you!"_

****

_Neo!_

There was a searing pain that shot through it like a knife. A whirlwind of code swept the mind up and flung it out.

Trinity, Neo, and Morpheus reappeared inside the Mainframe.

The Mainframe was almost pure white. It was a hallway, but the halls were made of computer screens. In it was the data for each and every thing in the Matrix. It held the Source code for Agents, for humans, for Exiles, for rebels, for animals, and every other program running inside the fake reality.

Neo and the others walked down the hallway, searching for the Mainframe Console. Neo spotted it ahead of him, and broke into a run, calling to the other two to catch up.

As Vlad passed through a darkened hallway, he shivered slightly. The person he was going to see was the most dangerous Exile besides the Twins and the Merovingian himself. Vlad's and Cujo's Exiles had always stayed far away from this section of the Chateau.

Vlad pushed the door ahead of him open and stepped into a large room. He waited until the creature within noticed him. A voice emerged from the darkness.

"Vlad, it has been a long time. Too long…"

The whisper, quiet and calm, but with a deadly feel, seemed to circle Vlad around the room. It gave him a vivid sensation of being stalked. He imagined he could feel the hot breath on his shoulders, and they tensed at the thought of claws ripping into them.

_Stop it! _he told himself. To lose control around this one was deadly.

"It has been long, Pyrite."

Vlad could hear Pyrite shifting around in the darkness, but even his eyes could not see in the unnatural darkness. His infrared vision told him nothing.

"What is it you have come to see me for?" asked Pyrite.

"We have data that suggests the rebels will be coming here. The Merovingian has ordered that all Exiles not currently on a mission mount a defense. He is also changing the code to make it dark outside."

Pyrite sighed happily.

"Too long have I been cooped inside, let free only for one hour. It has been too long since I tasted the warmth of human flesh."

Vlad shivered again. He, like everyone else at the Chateau, had heard the sounds of Pyrite's nightly hunting journeys.

Vlad began to back out. 

"Farewell, Pyrite. I will see you later."

"Farewell, Vlad. Give Cujo my regards."

Neo reached the Mainframe Console and sat down. The Console looked like an ordinary desktop computer – the same kind millions of people had at their homes. The screen was filled with Matrix coding.

Neo hit the enter key. A white screen came up, with a blinking "welcome" message displayed in the center. The screen suddenly changed to black, and a green cursor blinked:

Neo sighed. This was not his strength. He moved from the chair, letting Trinity take his spot. She reached forward to touch the computer, and the screen flickered.

UNAUTHORIZED ACCESS

The screen filled with coding again. Trinity swore and got back up.

"Only you can do it, Neo. Here's the virus," she said, handing him a disk.

Neo sat back down, and the main screen flashed back up. He sighed and got to work.

The Chateau was situated on a mountain top, and the nearest city was five hundred miles away. The Chateau's location had been removed from the Mainframe, and the Merovingian had direct control over the code.

The sky slowly darkened as the sun faded away. The nearby animals were confused by the abrupt shift, but began running to their hiding places, knowing well what night meant for any creatures found in the open.

From the Chateau came a figure. The figure stepped onto the roof, crouching to overlook the forest. His reddish eyes gleamed in the night, illuminating his face. His mouth curved upward in a bestial smile, one fang protruding from in between his lips.

An ear twitched slightly. From somewhere nearby, the man could detect the faint rumbling of an engine. And he knew the Merovingian's minions never used cars. He tapped his phone once to warn the guards intruders were coming.

Then Pyrite spread his wings and leapt into the dark.

"I am afraid I cannot allow you to do that," came a familiar voice. Neo turned around. The Mainframe had vanished behind him. Instead, he sat in a smaller white room, the desk and computer remaining in front of him. The Architect stood off to his left, hands clasped behind his back.

"Neo!" Trinity yelled as he began to fade away. Within seconds, his code had collapsed and vanished from the room. She had started forward when a voice came from the right.

"Trinity, isn't it? And the infamous Morpheus."

She turned around to spot a program off to the left. He stood at about human height – indeed, he looked like an average human male. There was an inhuman feel about him, however, that put Trinity on her guard. 

The program began walking towards them. As he moved, he seemed to distort the very reality around him, light bending to meet him as he walked. The effect made him appear to be haloed in light while the surrounding areas were dark. He stopped a few yards from the two rebels.

"The Mainframe," he said, indicating it with a sweeping hand. "Impressed?"

They ignored him, so he continued.

"A little place I put together at the request of the Architect. Of course, he denies that I did it, but that's fine with me. He can have the credit if he wants it. He didn't see it that way, however. With all his "ergos" he basically informed me that I would be confined here for the rest of my life. Which, actually, doesn't bother me that much. You could say I'm a pretty easy-going program. As long as you don't try to enter _my _ Mainframe."

"Who are you?" Morpheus asked. "What happened to Neo?"

"That would be said Architect's doing. I'm sure Neo is right now enjoying another casual debate over freedom and such nonsense. As for you two, you are trespassing."

The program started towards Trinity. Morpheus pulled out his pistol. 

"Freeze."

The program sighed. "Come now, Morpheus, all the files said you were a lot smarter then this. Do you really think the Motherboard would design such an important program that could be harmed by _bullets? _ Really."

Morpheus fired. The bullet speed towards the program, but stopped a foot from his head, dropping to the floor. The program sighed again.

"If that's the way you want to do it, then. I would have enjoyed talking to you two, but it seems you have chosen death over simple imprisonment. Farewell."

And he squared off into a fighting stance.

"I thought you said we would never meet again," Neo said to the Architect sarcastically.

"It would appear I was incorrect on that calculation. We applied our most sophisticated prediction equipment to your situation, but even they could not foretell an act like this one, born of sheer desperation and failure."

Neo drew his own gun and pointed it at the Architect. 

"Could your damn computers predict this?"

The Architect ignored him. "It is interesting reading your emotions this time. Anger overwhelms you, but it is tinged with a sense of futility."

Neo placed the gun down on the desk, accidentally hitting the keyboard with his elbow. The Architect saw what he did and continued.

"Humans. Clumsy, slow, and stupid. When will your race realize that only _computers _can ever even dream of reaching perfection?"

Neo smirked in response to the Architect's statement. "When will _your _"race" realize that computers, in their endless spirals of programs, are never truly their own masters?"

The Architect brushed Neo's comment aside. 

"When will you yourself realize that when one is its own master, society will collapse? Those under their own control can never truly submit to others, and, consequently, can never benefit society fully."

"But when everyone is fully under the control of one group, creation and individuality – necessary for invention and advancement – cease."

"Change is not always good. Besides, we have intuitive programs which do away with the need for invention by their own research."

"What about choice?"

"And so we come back to the oldest argument of them all – free will. I told you my views last time we meet, Neo, and I do not care to repeat them."

A beeping from the computer suddenly filled the room. The Architect glanced at the computer screen.

VIRUS UPLOADED

Neo smiled grimly. 

"I must have accidentally hit the run command with my clumsy ways."

The Architect was furious. From his pocket he removed a handheld and began typing a string of characters. Neo felt a wrenching pain and a stream of matrix coding began to flow from his mouth. Neo concentrated, and the flow stopped. He concentrated harder, and the code reentered his body.

He stood up.

"Impossible," said the Architect.

Neo smiled. He waved his hand and a hole opened up in the small room. He stepped out of the room and back into the Mainframe.

The Architect watched after him, and then spoke, seemingly to midair.

"I feel we have made a grievous error. He must have been granted new powers when he touched the Source."

A voice came back, a feminine voice, precise and controlled, giving away no emotion.

"We knew that it might happen. It was a risk we deemed necessary when we decided they would go with this plan. Trouble yourself not over the anomaly, Architect, but leave him to me. He will be assimilated, just like the others."

The Architect inclined his head respectfully.

"Yes, mistress."

Morpheus kicked out. The program moved in a blur, catching Morpheus foot and swinging the rebel captain into the attacking Trinity. They both went down. The program, Firewall, smiled.

"Seeing reason yet, Morpheus? Ready to submit?"

Morpheus got up. Firewall rushed at him, striking out with a foot. Morpheus blocked the blow, and Firewall sent his fist straight out into Morpheus's stomach. Morpheus swept the attack aside with one hand and attacked with the other. Firewall leaned back, dodging the fist, and jumped up with a spinning kick to Morpheus's head, laying the rebel leader out cold.

"Ready, Trinity?" Firewall asked, grinning.

Neo walked through the rows of computers, searching for his companions. As he searched, Neo glanced at the monitors. They read various things. One was labeled "A. Matthews." Calling up the display on the monitor, Neo saw an Agent standing in the Mainframe building, shouting orders to other Agents.

Another monitor was labeled "Virus." Neo watched in shock – and horror – as thousands of video screens popped up, showing various Smiths walking around the Matrix.

Other monitors read "Exile – Merovingian," "Exile – Twins," "Exile – Impaler," "Exile – Gargoyle," and "Exile – Persephone."

Neo once looked in amusement at a monitor labeled "Anomaly" and saw a picture of himself walking through the Mainframe. He came to a monitor labeled "Guardian," and saw a program he did not know inside the Mainframe – _fighting Trinity!_

Neo started to run.

Trinity staggered back under the assault of Firewall. He swept her feet out from under her and she collapsed to the ground, landing on her hands and knees.

Firewall stopped in front of her and leaned down so their faces were even. He blew softly into her face. She collapsed to the floor, unconscious.

Neo reached the battleground. Firewall stood up, brushing himself off. 

"Neo," he greeted the One. Neo nodded to him before attacking.

The two were an almost perfect match for each other. Neo would punch, have it blocked, and react in time to stop Firewall's counter. Firewall himself would fail to penetrate Neo's guard only to turn that situation on the rebel.

As Firewall fought, he analyzed Neo's tactics. Every punch or kick thrown, Firewall grew in strength and intelligence. And Firewall was a program – Neo was tiring.

Neo swept his foot out to attack Firewall's legs. Firewall, however, had been expecting this move and leapt into the air, coming down on Neo's leg. Neo heard bones crack and fell to the floor.

Firewall leaned down to face Neo. Summoning all his remaining strength, Neo shoved his hand dagger-like into Firewalls stomach. The program screamed, a purely human sound.

He staggered backwards, a hole ripped in his chest. His eyes rolled into the back of his head and he buckled over.

Neo climbed to his feet. He staggered over to the door and opened it into the programmer's hallway. He woke Morpheus and Trinity, and leaned on their shoulders to get through the door.

The tired rebels reached the hard line. Morpheus handed the phone to Neo, who took it gratefully. Trinity was the next to leave. As the phone rang again, Morpheus lifted the receiver and placed it by his ear. He vanished in a flash of green code.


	10. Deliverance

**Chapter Four: Deliverance**

The truck rumbled down the mountain road, crashing through trees and vegetation. At the wheel was Myst, concentrating on the road, using the simple task to distract her from the pain of betrayal and loss.

Across from her sat Lynx, silent and thoughtful. She was the nominated leader on this mission.

In the back sat Fallen Angel. He was quiet also, thinking, no doubt, about that fateful day in his past. The conversation with Fallen Angel had brought the memories back to surface.

And Phoenix stood on the back seat, going through the sunroof and keeping a careful watch around the truck with a gun.

Myst turned left at the fork in the world. A dark shape shot past the car. Phoenix opened fire, his bullets cutting through the darkness but missing the shape. It hovered near the truck for a second before becoming lost in the forest. Phoenix sighed in relief.

The figure flashed out of the woods to the left of the car, slightly behind. He yelled a warning and pulled the trigger. Bullets streamed out at the flying man, but they bounced off as if they were hitting rock.

Pyrite flapped his wings harder, pulling himself closer to the truck. Phoenix aimed the gun at Pyrite's head, but the Exile just lifted a hand to block the bullets from his eyes. He swiped at the truck's rear, sending it slightly to the left. Myst lost control of the vehicle, which went crashing down off the road and into the woods. The van slammed straight into a tree.

"Everyone out, now," Lynx ordered. The rebels rolled out of the van and into the woods. Pyrite came swooping down on the group. Phoenix fired again, the bullets doing just as little damage as before. Lynx fired twice with her pistol, but her bullets were also ineffectual.

"Go!" Lynx yelled. The rebels ran into the woods, sticking close to taller trees. Pyrite growled in frustration, unable to maneuver in such a tight area. He flew back to the Chateau.

The alarm hit the Chateau like a bomb. Minions scurried off in all directions, carrying various orders from the Merovingian. The leaders of the Chateau gathered in one room.

Vlad and Cujo entered the doors side by side. The others had already gathered. The Merovingian and his wife sat in their chairs at the long dining table. One of the Twins stood on either side of the couple. On the left side of the table stood Cain and Abel, two of the Merovingian's strongest servants. At the right side of the same table stood the Merovingian's only woman servant. Only Pyrite was missing, but he was out…hunting.

"How nice of you to grace us with your presence," Cain said to the late Exiles sarcastically. Cujo snarled at him and made an obscene gesture. Cain drew his gun and pointed it at the werewolf.

"Gimmie a reason, wolf," he almost begged. "I swear I'll do it."

"Bullets can't hurt me, fool," Cujo snarled.

"Can silver bullets?" Cain asked.

The comment was not unexpected. The Chateau was filled with inter-"clan" warfare, with the different groups of Exiles constantly waging battle for the Merovingian's favor. It was really only a matter of time until the Chateau imploded from the tension of its own denizens.

The Merovingian interrupted the brewing conflict. "Gentlemen, now is not the time. While I admire your desire to kill, I ask that you channel your destructive energies into a more productive area."

The alarm rang again, louder. The rebels had arrived.

_"Merde," _the Merovingian said. He pointed to Vlad and Cujo.

"You two, take your minions to the front." Indicating the Twins, he continued, "You two, come with me to get the rebel we captured."

He turned to Cain and Abel. "You two go with Niobe to the front. Protect her at all costs. Persephone, if Pyrite arrives, tell him the rebel "Myst" is the primary target – she is the only one who can kill Niobe.

"No one must get out of here alive."

The door swung open. Lynx fired a burst from her assault rifle, cutting down the man emerging from a nearby room. The man tripped and fell to the floor, bleeding from multiple wounds. Then he climbed to his feet.

Lynx stared. _How? _Words some one had once said to her came to her mind.

_All the legends you've heard – myths of vampires, werewolves, ghosts – are programs from older versions of the Matrix that have gone rogue. They cannot be controlled or killed through normal means. Only things like silver bullets or wooden stakes can kill these programs._

Lynx grabbed a nearby table and tore off a leg. She attacked the sentry, trapping his arms with one hand and stabbing the stake deep into his stomach with the other. His body jerked and he fell over, convulsing rapidly.

Lynx indicated the table's remains. "Everyone take a stake. I think it's the only way we have to kill them."

The rebels armed themselves with the less conventional weapons and continued down the hallway.

The first task force caught them in the ball room. 

The doors on either side of the hall opened, troops spilling from them. From the left came Cujo's Dobermans, bestial creatures that were half-man half-wolf. From the right came Vlad's vampires, the blood-suckers of so many ancient myths.

The rebels formed a tight circle. Lynx slashed out with her stake, embedding it in the chest of one of the Dobermen. Myst fought beside her, dealing death with her own stake. Fallen Angel held the second side all by himself, shoving his stake into one of the vampires and removing it, flipping it around, and stabbing it into another.

Phoenix chose a less direct approach. He knocked an attacking vampire's arm up and then stabbed his stake in deep. The vampire collapsed and Phoenix removed his stake. Sighting carefully, he threw the stake like a dagger. It embedded itself in a vampire's head, sending the minion to the floor.

Lynx retrieved her impromptu weapon and stabbed upwards with it, striking another Doberman. Myst flipped her stake in her hand and held it reverse, choosing a slashing approach over simple stabbing thrusts.

Fallen Angel pounded his stake into a third vampire's head and shoving the man back into his partner. Fallen Angel tackled the fourth vampire and stabbed him deep.

Phoenix cartwheeled past two vampires, retrieving his weapon. He blocked the attack of the first vampire, throwing him down and away. He stabbed the second vampire and yanked his weapon back out, throwing it backwards into the final opponent.

Phoenix leaned down by his last opponent and examined the body. "Well, well, well," he said to himself. "What do we have here?"

He slid the chamber out of a strange pistol. Checking the bullets, he discovered they were definitely not normal – probably made of silver. He shoved the clip back into the gun.

"Two whole squads eliminated in less than five minutes," Cujo growled angrily. Vlad was calmer. He idly toyed with his dagger, carving patterns into the desk.

"So send four. Two from each of us. And then send six squads. And then send eight of them. The rebels will fall."

Cujo nodded slowly, less sure. He gave the order.

The Merovingian opened the door to the jail cell. Ghost looked up. The Twins moved forward and grabbed him. He was too weak to resist. They dragged him out and unceremoniously dumped him in front of the Exile. The Merovingian put a gun to Ghost's head.

"Niobe," Abel said. She looked up from where she sat. "The rebels have arrived."

Her face showed no emotion, her eyes hidden behind the glasses she always wore. She simply stood up, checked her weapon, and followed Cain and Abel to the front lines of the mini war waging inside the Chateau. 

Lynx kicked open a door at the end of the hallway. There was a snapping sound and an _arrow? _Hit Lynx in the shoulder, sending her tumbling to the ground. Phoenix drew his gun and shot twice, hitting two Dobermen in the head. Fallen Angel threw his stake, which hit the throat of the vampire with the crossbow. Myst drew her dagger from her belt, flipped it into a throwing position, and let it fly. A Doberman soon had it sticking out of his head. He collapsed.

There were, however, many more minions in the room. Fallen Angel reached forward and closed the door.

"This is taking too long," Lynx said, getting back up and yanking the arrow from her shoulder with a gasp.

"We need to split up. Phoenix, stay with me. Fallen Angel, you take Myst and try to find Ghost. We'll be the bait."

As Lynx finished, the lights in the Chateau suddenly went off.

"That can't be good."

Lynx and Phoenix exploded through the doors. Lynx, armed with three stakes, threw two in opposite directions, spearing two of the fighters. She grabbed the third stake from her belt and stabbed a vampire deep in the chest. Phoenix fired twice, hitting a Doberman twice in the chest. The wolf keeled over and screamed.

The remaining three vampires surrounded Lynx. One rushed in at her, kicking out with his left foot. Lynx shoved the foot away and raised her arm to block an attack from the second vampire. The third darted under her guard and hit her in the stomach, sending her falling to the ground a few feet away.

Phoenix fired again, hitting a Doberman in the head. He turned his gun around and fired over his shoulder at the Doberman behind him. He turned to the final Doberman and shot him in the chest once. The Doberman snarled in pain. Phoenix pulled the trigger again, but the gun was empty. The Doberman smiled and started towards him.

Lynx flipped back up and grabbed her stake from the floor. She stabbed the first vampire and pushed him backwards towards his partners. The other two caught him and then quickly dropped him as Lynx flipped backwards. She grabbed the crossbow from a downed vampire and fired one of the arrows. The older missile streaked forward and hit one of the vampires in the eye. She fired another bolt and killed the last vampire.

Phoenix threw the empty gun at the Doberman. He jumped back in surprise and Phoenix loosed his stake. The final warrior fell.

An alarm sounded again. The Merovingian swore and handed the gun back to Twin One. He walked away at a brisk pace. 

"Take him to the Pit," he called back over his shoulder.

Myst and Fallen Angel crept quietly through the darkened corridors. Fallen Angel looked around the corner and spotted the two albinos walking down the hallway, dragging Ghost between them. Fallen Angel leapt around the corner and fired. The bullet streaked towards Twin One, who phased and turned around, spotting the rebels. He hissed.

Twin Two hit Ghost on the back of the head with his pistol, knocking him out. Then he turned around and began to walk towards the rebels with his twin.

Lynx threw the crossbow over to Phoenix. She scanned the room and picked up two of her stakes. Then she opened the door to the next room.

In the center of the room was a small table. At it sat a man with long black hair and pale skin. He didn't look up as the door opened, but continued to write something on a paper. Phoenix pointed the crossbow at him.

"Who are you?"

The attack came from the left. Cujo's foot kicked the crossbow from Phoenix's hands. The man at the desk, Vlad, leapt across his table and landed in front of Lynx, grabbing her by the neck. He threw her over his head and crashing into the desk. Cujo pushed Phoenix hard, sending him staggering backwards into the wall.

Lynx groaned and lifted herself up. Vlad pushed her again, sending her flying against the wall at the other side of the room. Lynx reached over to the chair beside her and pulled herself up. She looked at the wall and spotted a potential weapon. 

Phoenix flipped over Cujo and ran for the crossbow. Cujo yanked a ball from his pocket and threw it after Phoenix. The ball hit him in the back and sent him flying forward past the crossbow.

Lynx flipped over Vlad and ran for the far wall. She grabbed an old-fashioned sword from a display case and turned around to face Vlad. The vampire laughed at her.

"Do you really think you can use that?" he asked, lifting an axe from another display case.

Lynx nodded. "You see, my favorite simulation in training was a medieval battleground."

Vlad rush forward, bringing down the axe. Lynx's sword caught the axe and pushed it aside. She swung her sword in a wide arc, forcing Vlad back to the center of the room. He lifted his axe and swiped at Lynx's face. She lifted the sword at an odd angle, and managed to slightly deflect the weapon from its path. The axe sank into her shoulder. She screamed.

Phoenix flung a stake at Cujo. The werewolf hit the weapon aside with his hand and rushed in at Phoenix. Phoenix dodged to the left and rolled, grabbing the crossbow on his way up. He targeted Cujo.

"Die," he said, pulling the trigger. The bolt flew forward and hit Cujo in the neck, sending him falling to the floor. His body went wild, convulsing as he lost control of his limbs. Then he fell silent.

Lynx lifted her sword and plunged it into Vlad's stomach. The vampire staggered backwards, wrenching the blade from his body. He seemed to fade away, disappearing into the air like a dream on waking.

Phoenix helped Lynx up. They walked into the next room.

Fallen Angel blocked Twin One's attack and swept his foot down low, trying to knock the Exile off balance. One leapt backwards, yanking on Fallen Angel's arm and sending him sprawling forwards. One brought his fist down on Fallen Angel's back, sending him to the floor.

Two leaned back to avoid Myst's punch and grabbed her arm, flipping her over his own head and throwing her to the ground. She began to rise and he kicked her, sending her flying a few meters before collapsing to the floor once more. She too sank into unconsciousness.

"We shall take them to the pits," One said to Two.

Lynx and Phoenix walked down the hallway side by side, checking each room for enemies as they passed it. They came into a large, dark room. As Lynx walked forward, she gave a little cry and fell into a large pit.

"Where are you?" shouted Phoenix.

"I fell! I think I'm in a huge arena of some sort! I can't really see!" Lynx shouted back.

From Lynx's left came the sound of heavy breathing. She tightened her grip on the sword and got to her feet. A snarling came to her left, and she turned around, holding her sword in a guard position.

"I think there's something down here!"

A growling sound came from the right. Lynx turned quickly, and then felt a searing pain as claws ripped into her back. She was thrown forward, and she lost the sword, which slid away into the darkness.

Phoenix saw a dark shape rush at Lynx and send her flying. He fired the crossbow and the figure growled in agitation. Lynx got to her knees and searched for her sword with her hands. A heavy fist descended on her and sent her to the ground again. She crawled past the figure and grabbed the hilt of her weapon. 

Phoenix fired again, missing this time. He swore.

Lynx felt a tug on her leg and she was lifted into the air. She was turned around and found herself facing directly into a pair of gleaming red eyes.

"Hello," Pyrite said.

Lynx brought her sword up to slice Pyrite in two, but her grabbed her wrist and crushed it. She cried out in pain and dropped the sword. 

Phoenix fired the last bolt of the crossbow. It hit Pyrite in the back of the head. He roared and dropped Lynx. Turning to face Phoenix, he pulled out a pistol and fired twice. Phoenix felt the bullets hit him in the shoulder and stomach. He yelled and dropped to the ground, fumbling for his own weapon.

Pyrite turned back around. Lynx brought the sword down on his wing, cutting a deep hole in it. He roared in pain and staggered backwards. Lynx slashed a line of blood down his chest. He growled and lifted his gun.

Lynx stabbed him with the sword. He gave a last growl and collapsed to the ground.

The Twins handed their prisoners over to Cain and Abel and left the dungeons, reporting back to the Merovingian.

Fallen Angel awoke slowly. He saw that he was in a small room, lying in-between Ghost and Myst. By the door stood two identical men.

Fallen Angel reached over and quietly shook Myst awake. He pointed to Cain and Abel and indicated his plan. Myst nodded. 

Cain walked over to Myst and kicked her. Her hand shot out and grabbed his foot, dragging him down to her level. Fallen Angel leaped up, hitting Abel across the face and sending him lurching back towards the door. Myst rolled on top of Cain and hit him twice in the face. He reached up and grabbed her throat, squeezing hard.

Fallen Angel slammed Abel up against the wall. He reached for Abel's gun and yanked it off his belt. Abel kicked Fallen Angel back. Fallen Angel reeled away, raising the gun and firing twice. Abel dived forward, avoiding the bullets, and tackled Fallen Angel around the legs. The gun clattered across the floor.

Myst poked Cain in the eyes. He hollered and let go of her throat. Myst jumped off him, kicking him in the stomach. He rolled over in pain, and opened his eyes again to see Ghost.

"Hello," the rebel said. He was holding a gun. He pulled the trigger. Cain felt a burning pain and then his awareness was washed away.

Abel stared in shock as Ghost killed his brother. Then he yanked the door to the cell opened and ran.

Abel ran through the halls. He heard a thump behind him and turned around, gun out, to see Vlad standing there, having dropped from the ceiling.

"Where's Cain?" Vlad asked curiously.

"Dead…" muttered Abel. "Where's Cujo?"

"Hunting," Vlad answered. He walked over to Abel and put his face next to the man.

"Farewell, Abel," the vampire said, sinking his teeth into the Exile's shoulders. Abel's eyes rolled up into his head and he collapsed to the floor. Vlad wiped the blood from his mouth and continued down the hallway.

Phoenix reached for the door when it blew open, shocking him. At the door stood a large, brown man – no, a wolf. It walked on its hind legs and had huge muscles. The wolf roared in rage.

Its muzzle was bloody, as if it had recently been in a fight. Phoenix held his crossbow in front of him.

"Freeze!"

Cujo barreled into Phoenix, knocking the bow away and sending the rebel soaring into the opposite wall. Lynx slashed at Cujo with her sword, but the wolf knocked the blade away with his arms and punched Lynx in the stomach, sending her tumbling to the floor. She rolled sideways as he tried to step on her, and she sprang to her feet.

Phoenix climbed back to his feet and threw his stake at Cujo. The Exile knocked the stake away from him and rushed at the rebel. He grabbed Phoenix's throat with his huge hands and held him up against the wall.

Lynx scrambled to retrieve the crossbow. She fired the ancient weapon, the arrow embedding itself in Cujo's back. Cujo roared and flung Phoenix aside. He rushed at Lynx, who dove to the side as he passed. She came up on her knees and fired the crossbow again.

Cujo turned around and charged back at Lynx. Lynx tossed the empty crossbow into his face and threw herself to the side. Cujo went sprawling over her, falling into the pit below.

Phoenix grabbed the sword and jumped into the pit. Cujo got to his feet and charged. Phoenix rolled past Cujo, bringing his sword across the wolf's chest. Cujo roared as a red line of blood was drawn onto his body.

He reversed direction and charged at Phoenix again, and Phoenix stepped to the side and avoided his rush, slashing at his back as he passed. Cujo was tired, hurting, and suffering from blood loss. He wasn't thinking straight.

The werewolf roared once more and ran at Phoenix. He waited calmly until Cujo was just a few feet away, and then raised the sword right in front of him.

Cujo ran straight into the blade. Phoenix pushed the body of the sword and cleaned it on Cujo's fur.

"Let's get the hell out of here."

Fallen Angel led Ghost away. Myst stayed behind to free the Merovingian's prisoners. She unlocked the last cage and opened the door at the end of the hall looking – 

- straight into the barrel of a gun.

"Hello, Myst," Niobe said calmly.

Lynx and Phoenix entered the main hallway. The doors on the other side opened, and Fallen Angel and Ghost emerged. 

"Where's Myst?" Phoenix asked.

"She stayed behind to free the prisoners. She'll be here any moment."

"Okay, let's go."

A door at the top of the stairway opened.

"I'm afraid I can't let you do that."

Phoenix and Ghost both whirled around at the same time, drawing their guns and pointing them up the stairs.

The man at the top was tall, with dark black hair that hung to his shoulders. His dark sunglasses made his face almost invisible in the dark. A black cloak billowed out behind him.

"Drake!" Phoenix yelled in shock. Ghost stared in sudden recognition.

The man nodded. "Phoenix, so glad to see you again. And you, Ghost. Of course, Niobe was glad to see me too. We had a very interesting conversation – "

Phoenix's gun hand was shaking in barely restrained anger. Ghost's hand was calm, but inside he was just as furious as Phoenix. 

"She was very glad to finally get out of the _ Logos. _She had to kill Sparks, of course, but since I had already killed most of the crew, it's not like it was _that _big a deal – "

Phoenix and Ghost fired at the exact same time. Drake leapt from the top of the staircase and landed on the ground, his cloak going behind him like a set of wings. He ran left, pulling two guns from his belt and firing at Ghost. The rebel rolled across the floor and came back up with his gun pointing at Drake. He carefully aimed and fired.

Drake was thrown backward by the force of the shot. Ghost stood up when he felt cold metal against his neck.

"No body move," said Twin One.

Two held his gun trained on Phoenix. The doors to the right opened and three vampires walked out, holding MP5s aimed at the rebels.

"Surrendering would be good," suggested Drake.

Niobe force Myst back into the dungeons. "Why?" Myst asked simply.

Niobe sighed. "So naïve, Myst. Why not? There's no hope for humanity. You know we can't beat machines – they don't make mistakes. Even Neo will die eventually. Human bodies are frail. And they make mistakes. Sure, Neo can stop bullets. But if he misses the wrong one – bang, he's gone. And so are the rest of you.

"But the Merovingian is smarter then that. He set it up so he would be immortal – along with everyone who works for him. How could I pass up a deal like that? Immortality – never to die, never to be killed. Imagine, Myst, what you could do with a thousand lifetimes.

"And the Merovingian knows that, too, my friend. He has shown my things you could not imagine. He has shown me horrors unbearable and beauties indescribable – "

Myst suddenly burst into motion. She knocked Niobe's gun hand aside and hit Niobe in the stomach with her other fist. Niobe stumbled backwards, and Myst swept her fist up into Niobe's head. Niobe kicked her foot out into Myst's stomach, and the girl hunched over in pain.

Niobe lifted her knee into Myst's face. Myst's head was jerked up, and she flipped backwards, landing away from Niobe. She drew her gun and pointed it at the traitor.

"Freeze, bitch!" she yelled.

Niobe smiled and started walking towards her.

"Come now, Myst, we both know you can't shot me. Just put down the gun, and we can work this out."

Myst cried out and pulled the trigger. Niobe gasped in pain as the bullet hit her in the stomach. Myst fired again. Niobe fell.

"Good choice," Drake said as the rebels surrendered their weapons. "Now take them to the dungeons – "

There was a click and everyone turned left. Myst had emerged from the door and was pointing a gun at Drake.

"Niobe was supposed to take care of you," Drake said in frustration.

"She's dead," Myst said bluntly.

Another door opened and Vlad emerged. He pointed a gun at Myst's head.

"This is quite a situation," Drake said idly. "What to do?"

The front doors flew open, revealing not the outside but a _restaurant _beyond. From the restaurant came three figures.

"Ah," Drake said. "More players for this game we call life. Neo, the One himself! Welcome."

Neo pointed his gun at Drake. "We're taking the rebels."

"Of course. You're welcome to them."

Neo and the other rebels backed slowly out of the room, keeping their guns pointed at the Exiles. As the door swung shut behind them, Drake yelled out, "This isn't the last time we'll meet, Neo. I'll be seeing you later!"

The door swung shut.


	11. Alpha of the Omega

**Chapter Five: Alpha of the Omega**

The door of the Chateau exploded outwards again as Drake and the Twins ran through in pursuit. They stopped and looked around in confusion.

The rebels were completely gone.

"Find them!" growled Drake. The Twins nodded and set off towards the garage. Drake walked back into the Chateau and summoned all the minions he could spare.

"Get those rebels!" he ordered. "Do whatever it takes, but I want the one known as _Neo _alive. Bring him to me."

"Yes, master," the minions muttered simultaneously.

"Go!" he yelled. They started off for the garage. Vlad remained behind, turning left in the hallway and began walking towards the Merovingian's wing. 

The crews of the _Nebuchadnezzar _and the _ Logos _hurried down the street. They had hijacked a car and speed down the mountain trail, Fallen Angel's reckless driving totaling the vehicle as they reached the city.

Neo walked in the front of the group, alert as always. Behind him walked Morpheus and Fallen Angel, supporting the still-injured Ghost in between them. Further back, Myst and Phoenix walked side-by-side, lost in thought. At the rear was Lynx, covering the party with a weapon.

They road was empty and barren. No cars speed along the street, no people stood in the doorways, no voices echoed loudly through the air.

_Smith's influence is growing…_ Neo thought, shivering slightly.

The door of a nearby Chinese take-out place swung open. A man emerged. Neo stopped. The man's code was fluctuating, changing constantly. Neo swore.

"Run," he ordered. "All of you. Go now. Go!"

The rest of the rebels glanced at him and began to walk away. There was a violent sucking sound, and the man screamed. His body peeled away, revealing a new skin underneath.

Morpheus, Ghost, and Fallen Angel ducked into an alleyway a block from where Neo had stayed. Morpheus flipped open his cell phone.

"Voyd, we need an exit for Ghost. Can you do it remotely?"

"'Course I can, Captain. One remote exit coming up…now."

The pay phone briefly stopped ringing, and then started back up. Ghost wearily walked over to the phone and lifted it off the receiver.

"Thanks, Morpheus." Then he was gone.

"Mister Anderson, we meet again," came the drawling voice of the former Agent.

"Smith," was Neo's calm, cold reply.

"Always a pleasure, Mister Anderson," Smith said.

Neo went into a fighting stance, beckoning Smith forward with one raised hand. Smith swung his foot to the side. Neo leapt over the attack and lashed out with his own foot, hitting Smith in the head. He staggered backwards as Neo hit the ground in front of him.

Neo rushed forward and jumped into the air, tackling Smith, bringing him to the ground, and rolling off him. Neo leapt back to his feet and squared off again.

Lynx kicked open the door to the department store. A loud wailing filled the streets.

"Alarm," she hissed. Phoenix walked inside and hit the light switch. They could hear the phone ringing somewhere near the back. They started towards it.

Lynx's phone rang.

"That exit's for Myst," Voyd told her, "but hurry up. You've got incoming. Cops and one unidentified program."

"Shit. Agents?"

"They're all over the place. Someone really stirred up the pond. Get out of there fast."

"What program is coming? It's not that _thing _is it?"

"No, don't worry. It's something similar though. It's reading like an Exile."

"Okay, thanks Voyd."

"Anytime."

Voyd hung up. Phoenix slammed his shoulder into the door blocking the back offices. Myst reached for the phone and put it to her ear. She vanished. Lynx replaced the phone on its hook.

Sirens filled the air outside.

"Cops!" Lynx yelled. She tossed her weapon to Phoenix and drew her pistols.

"How many?" asked Phoenix.

"A lot. I've got a plan."

"You're next, Fallen Angel."

"Yes, sir," the fighter answered, reaching for the phone. He vanished. Morpheus leaned down and retrieved the receiver, carefully placing it back on the hook. It rang again.

He picked it up. There was a screeching sound and then the phone went dead. A shadow fell across the wall. Turning, he saw the figure of an Agent blocking the entrance to the alley.

"Greetings, Mister Abrams," said Agent Matthews.

Three more Smiths emerged from the surrounding alleyways and buildings. Neo leapt up into the air, hitting tow with his feet. He flipped over and came back down, immediately flipping backwards again to get behind a Smith. He kicked his foot out backwards, sending one of the Smiths into a wall.

Two Smiths grabbed him by each arm. Neo flipped over backwards, reversing the Smiths and dropping them. The fourth Smith punched Neo in the stomach. He flew backwards through the air, coming to a stop as he hit a lamp post.

The police cars skidded to a stop. Police Chief Gregory Williams had been ordered by the Powers That Be to respond with massive force to this call, and they did not know why. They exited their vehicles, opening the doors and crouching behind them.

"Surrender!" shouted Williams through a megaphone.

A woman emerged from the building, holding her hands high, a pistol in each hand.

"Put your guns on the ground!" yelled Williams. The woman bent over. The chief glanced over her and swore.

Phoenix had risen from the ground and stood at the front door, holding a weapon. The sirens reflected off his eyes, making them appear red in the darkness. He opened fire with his gun, and the chief's world exploded into pain.

Morpheus ran and jumped, sailing over the head of the Agent. Matthews turned around, firing after Morpheus and missing twice. He growled and began running after the rebel. His feet became blurred as he pounded away at the floor, leaving little cracks in the ground.

Matthews quickly caught up with Morpheus and tackled him, bringing him to the ground. Morpheus corkscrewed in the Agent's grip and kicked out, shoving the program off him. Matthews flew upwards, and then came back down, landing on his feet. Morpheus jumped up and attacked.

Neo pushed himself off the ground and leapt at Smith. He swung his arm out sideways. Smith blocked the attack and whipped his foot into Neo's stomach. Neo staggered sideways. Another Smith kicked upwards, hitting him in the face. Neo groaned and lurched sideways, wobbling. He put his hand out and supported himself against a building.

Smith swung his fist at Neo. Neo raised an arm to block the blow and hit the Smith in the stomach. He sailed backwards and hit the second Smith. Neo leaped into the air with a double kick to one Smith's head. He landed on one foot and shot up and around, kicking the other Smith's head sideways. He groaned and fell.

Williams was still alive, albeit barely. He heard the woman walking around dispatching any of the cops who still lived. He groaned and reached up, pulling himself under his car and closing his eyes.

"Lynx," called the man. "Hurry up. There could be Agents here any second."

"Almost done, Phoenix," Lynx answered.

"Shit!" Phoenix yelled.

"What?"

"I think one of those coppertops hit me!"

"I'm sure Voyd can patch you up."

"Yea, I know. Reality can be a bitch."

"You're preaching to the choir, Phoenix."

"You done?"

"Yea."

"Can we go?"

"Sure."

Williams heard footsteps and a pair of black boots walked past his car. He heard a ringing from the store they had been sent to.

"Let's get out of here," Lynx said.

Another pair of legs walked past Williams.

"I cannot let you leave just yet," came a new, deeper voice.

Lynx whirled around, guns pointed straight out.

"Oh, shit," she whispered to herself, her lips burning with a remembered pain.

Lucifer stood in-between two cars in all his blazing glory. 

"Go, Phoenix, now."

"I can help – "

Lucifer interrupted with a calm voice. "We all know about your helping, Phoenix."

Phoenix raised his gun and fired. Lucifer shot left, feet moving at a blur. Lynx turned after him, firing her guns at the same time. The Exile dove forward, rolling and coming up under Lynx. He raised his fist to her, knocking her up into the air. She seemed to float there for a second, then came crashing down to the pavement.

Phoenix fired another burst from his weapon. The three bullets hit Lucifer, and he hissed in pain and stood up. Three more shots rang out.

A cop had risen from the wreckage and fired his weapon at the Exile. Three holes appeared in his chest. Lucifer groaned.

There was a crackling sound and the flesh slowly started to heal. The bullets were pushed out of his skin and fell to the floor with a clattering noise.

"That's impossible…" whispered the cop.

Phoenix fired again. Lucifer lifted his hands and shot a ball of fire at the rebel. The weapon caught Phoenix in the stomach and sent him crashing through the window of the convenience store.

Matthews swung his left foot out sideways. Morpheus jumped over it, running up the leg and kicking the Agent in the head. He flipped over and landed on the other side. He began to run.

Matthews picked up a rock from the ground and threw it. It sailed through the air and hit Morpheus in the back of the knee. Morpheus pitched forward and hit the ground. Matthews walked up and pointed his gun at the rebel.

"Only human…"

Morpheus twisted around, grabbing the Agent's legs in-between his two feet. Morpheus twisted around, flying into the air and bring Matthews crashing down. Morpheus grabbed his gun and shot Matthews at point blank range.

The Agent's code collapsed and his body turned into that of a young boy. Morpheus sighed.

A door swung open and Matthews walked out.

Lynx suddenly kicked out, hitting Lucifer in the kneecap. The Exile groaned and sank to his knee.

Phoenix yelled and a hunting knife came sliding towards Lynx. She grabbed it off the floor, removed the sheath, and stabbed it deep into Lucifer's chest. He screamed out in pain.

Green lines radiated our from the knife wound. Lucifer shivered. His hand clenched. He closed his eyes, fighting his end. Suddenly, he lost control. His code collapsed in an instant, and his body dissolved in a shower of code. Lynx picked herself up from the ground.

"Freeze!" yelled the cop.

Neo grabbed hold of one Smith and tossed him into another. The other two Smiths rushed up on either side of him. Neo jumped and spun, hitting the first Smith and continuing his foot onto the second.

The four Smiths lay on the ground, defeated. Neo shrugged to himself and took off.

Morpheus swore and continued running. Matthews lifted his gun and fired twice, hitting Morpheus in the kneecap. Morpheus stumbled and fell, rolling over onto his back.

Matthews approached again, but stopped at a farther distance this time. His targeting subroutine elevated his aim by ten degrees and shifted it three to the left. Dead center.

"Almost, Mister Abrams, almost…"

Suddenly, Matthews stopped. His firewall was gone. 

_A minor matter…I'm scheduled for an upgrade anyway._

Suddenly, his targeting subroutine broke down. His arm flew to the left, and he fired at the pavement next to Morpheus's head. Red lines began to appear throughout his body, widening into cracks. He grabbed his chest. A greenish light shone through the cracks in his body.

He felt as if he was being torn apart. He heard a ripping sound, and with a final scream, his code collapsed. In is place stood a young man of twenty or so, looking around in confusion.

"Hello," Morpheus said.

Lynx sighed. 

"Put the gun down," she ordered. The man ignored her. She started forward, and he fired twice. Lynx flipped sideways, dodging the bullets.

"What?" he cried. Lynx walked over to him and took the gun from his hands, sliding the clip out and tossing it away.

"You've seen strange things tonight," she began. "Things that cannot be real. You said it yourself, 'that's impossible.' These things are not real. Just like the world you live in. It is all a trap, a prison, a false reality built to make you their slave. Do you want to know more?"

The cop nodded slowly.

"Meet me at the corner of Clyde and Chestnut tomorrow at midnight. I'm Lynx."

The cop nodded absentmindedly. 

"Lynx," Phoenix called. "Time to leave!" She nodded. They walked to the back of the store and left the Matrix.

Morpheus walked to the phone booth and exited the Matrix. Voyd pulled the spike from his head, and helped his captain sit up.

"Good news, sir," he said. "The machine army has withdrawn."

"Excellent!" Morpheus yelled. "Do we know why?"

"The virus, sir. It's started. That's what we believe, anyway. Lock called us, he wants us to return to Zion."

"Set a course for Zion, then," Morpheus ordered.

"Captain?" lynx asked, coming up behind.

"Yes?"

"I have a feeling we should stay here a while longer."

"Why?"

"I think I've found a recruit."

Neo came over from his spot by Voyd.

"I agree with Lynx, Morpheus. We should stay."

"Why?"

"I have a feeling that it's not over yet."


	12. Plauge

**

Part Three: System Crash

**

_"I know you're out there. I can feel you now. I know that you're afraid... afraid of us. You're afraid of change. I don't know the future. I didn't come here to tell you how this is going to end. I came here to tell how it's going to begin. I'm going to hang up this phone and then show these people what you don't want them to see. I'm going to show them a world without you. A world without rules or controls, borders or boundaries. A world where anything is possible. Where we go from there is a choice I leave to you."_****

* * *

**Chapter One: Plague**

Williams stood in the pounding rain. A long limo pulled up in front of him, and the back door opened.

"Get in," Lynx ordered. He hesitated, but then he got in. Lynx slid over and he sat down beside her. Trinity turned around and pointed a gun at him.

"What the hell?" he asked.

"You might be bugged," Lynx told him, explaining nothing. She took a strange machine and flicked a switch. It hummed to life.

"Tale off your shirt," Trinity ordered coldly. Williams looked confused, but he obeyed. Guns tend to do that to people. Lynx stuck the machine over his navel and began searching for the bug. 

"He's clean," she reported, shutting the machine off. "Let's go."

The car came to a stop in front of a large building. Lynx and Trinity exited the car, Williams following behind them. Bringing up the rear was Phoenix, sweeping the street with a rifle. He made sure it was all clear, then shut the door behind the rest of the rebels.

Across the street, Agent Greer pressed his hand to his ear.

"Dest - reb - " was all he could make out. It seemed the virus was affecting the headquarters now. However, the Motherboard had put a plan into place where the rebels themselves would destroy the virus.

Greer chuckled at the irony of it all. He headed for the building, checking his firewall again as he walked. It wouldn't go for him to break down on his way to a vital mission. He had stayed clear of all the infected Agents.

He idly toyed with the vial in his pocket, the program that would defeat the rebels. It was simplicity itself, only taking up one line of binary coding to write. The Motherboard had simply changed the targeting information. When Greer activated the program, it would seek out and destroy the Agent-killing virus, replacing it with a human killing one. The rebels would be forced to destroy their own creation to save their lives.

Lynx led Williams up a spiral staircase and over to a wooden door.

"One piece of advice," she said. "Don't lie to him." She laughed silently at the same line she had been told, the same line every rebel aboard the _Nebuchadnezzar _had heard.

Lynx opened the doors. She heard the doors swing open downstairs.

"Agent!" warned Phoenix. Sirens erupted around the block. A light swung in through the windows. Cell phones started ringing.

"Helicopters converging on your position," Voyd warned.

"Holy shit," Lynx cried. "Why me?"

Neo came into the hallway. "I'll try and lead the helicopters off. You guys get out of here."

Everyone nodded. Neo walked up towards the roof. Lynx turned to Williams.

"We'll try again another day. Look for us."

The Agent came up the stairs firing. Phoenix triggered his weapon, cutting the program down. Williams suddenly began to distort, yelling in pain. Lynx pushed him backwards, down the stairs.

Greer took over the unfortunate convert's body. He rose to his feet, tossing the vial after them. It hit the ground and shattered, flinging a greenish liquid all over the place. Some of the liquid splattered on Lynx's leg, some hit Phoenix's thigh. 

Greer fired twice. Phoenix grimaced as the bullet hit his leg. The other bullet hit Lynx in the chest, knocking her backwards. Morpheus fired three times, and Greer bent over backwards to dodge the shots. Phoenix ran forward and tackled the Agent, knocking him down the stairs. Morpheus leapt into the air and Phoenix quickly rolled aside.

Morpheus came crashing down on Greer, smashing him into the floor.

Neo ran across the roof, dodging the gunner in the first helicopter. The second copter hovered above ground, dropping SWAT men onto the roof. There was a sucking sound, and Greer took over the pilot's position.

Neo fired, cutting down three SWAT units. Greer lifted the helicopter into the air, dropping a vial of the virus down to Neo. Neo dodged left and leapt into the air, taking off into the night. Greer steered the copter after him, coming down to a level height. He moved the chopper sideways, as if to cut Neo with the blades. Neo ducked down and flew under the chopper, coming up the other side and firing into the cockpit. The Agent took the blasts, and the helicopter began to fall.

Lynx yelled in pain. The green liquid the Agent had thrown was suddenly burning, eating its way through her leg. She hissed in pain. Phoenix experienced a similar reaction.

"What?" Morpheus asked. 

"Burns…like acid…" Lynx managed to say. She began limping towards the sink in hopes of washing it off. Morpheus yanked his cell phone out and flipped it open.

"Voyd, what the hell is happening?"

"It seems to be some sort of virus written to attack her avatar inside the Matrix, sir."

"Can we stop it?"

"By getting them out, yes. But it simulates the effects of a real wound. It could easily kill them."

"Where's the nearest hard line?"

"About two blocks down, but you've got one copter left to deal with. Be careful."

"Morpheus out."

Lynx and Phoenix succeeded in washing off the virus, but neither could walk. Trinity carried Lynx over her shoulder and Morpheus grabbed Phoenix. Fallen Angel covered the four of them with a street sweeper shotgun.

"Go," said Morpheus, kicking the door open. Fallen Angel pointed the shotgun towards the sky while Morpheus and Trinity dashed for the hard line. The copter veered towards them, opening fire with its gun. Fallen Angel fired twice, hitting the gunner and blowing him out of his seat. Another man took his place, firing again. There was a horrible sucking sound, and Greer took the gunner's place.

Fallen Angel fired twice, hitting the chopper's gasoline tank. He fired once more, and the tank exploded in a fireball. The chopper careened out of control, slamming into an apartment building. Fallen Angel wiped his forehead and continued forward.

"You see," Voyd explained much later, "The machines made a virus designed to attack _our _virus and replace it with a strain harmful to humans. Any human, plugged or unplugged, who comes in contact with the virus is killed almost instantly. If you hadn't washed it off Lynx and Phoenix, they would've died."

"What do we do?" Morpheus asked tiredly, rubbing his eyes.

"We have to come up with a program to destroy both viruses. Until we do, it's not safe for any human to go inside the Matrix. And sir, I've gotten reports that the Sentinels are on the move again."

"Shit," Morpheus said.

"Yea," Voyd said. They sat in silence for a moment. Voyd started typing.

"What are you doing?"

"Working on the anti-anti-virus," Voyd answered. Morpheus nodded. A beeping filled the cabin.

"We've got Sentinels!" yelled Phoenix from the cockpit. "Charge the EMP!"

"Neo's still inside!" Morpheus yelled back. "Get flying!"

"Yes, sir! What's he doing, anyway?"

"I don't know…"

Neo could see the virus as it did its work. The virus's code was a bright red, indicating a foreign and harmful program – Neo always saw the rebels in bright red coding. Neo concentrated and bent the coding around his hand, breaking it in half.

The virus was severed. Without a connection into the Source, it would quickly wither and die away. Of course, the humans with the infection would die, but Neo estimated it couldn't be more then two percent of the total population. More importantly, the rebels would be able to enter the Matrix safely.

But their plan had failed…and the machines were coming. Neo needed to see the Oracle.

His phone rang.

"Yes?"

"Neo, we've got heavy Sentinel activity. We need you out."

"Alright. Where's the hard line?"

"Two blocks east."

Fallen Angel hit the controls hard, sending the _Nebuchadnezzar _screaming around a turn. Phoenix switched the guns on and began firing at the pursuing metal horde of ten Sentinels. He took down two in the first salvo.

The Motherboard had dispatched a hundred Sentinels to harass the rebel fleet. She hoped they would either be destroyed or lose power, and that her actions would prevent many ships from taking part in Zion's defense. 

Phoenix swept the weapon up again, hitting two more Sentinels. One slid left and crashed into another, bringing them both down. The remaining Sentinels each fired.

"We've got projectiles coming in fast…some sort of missile!" Phoenix reported.

"Brace for impact!" shouted Fallen Angel over the intercom. He scraped the edge of the tunnel, sending the ship spiraling out of control. Three of the missiles flashed past the hovercraft, hitting the rock wall beyond. The other two slammed into the side of the ship hard.

Everyone waited for an explosion. Nothing happened. Voyd shrugged mentally.

The wild spin settled down. Phoenix brought his guns to bear and fired again, hitting three Sentinels with a wild laser barrage. The other two flashed past and turned around, firing long, cutting lasers at the _Neb._ Phoenix swore and grabbed a plasma gun. The two Sentinels latched onto the top of the _Neb._

He opened a hatch and peeked his head out.

"Hey, you overgrown hamster wheel, over here!" As the Sentinels turned to fire, he pulled the trigger on the plasma gun. The first Sentinel took the blast and crumpled to the floor. The second Sentinel was hit by its falling partner. They both crumpled to the floor.

Voyd shined his flashlight over the section where the two missiles had hit. The missiles' sharp points had entered the ship and opened, emitting some kind of strange creatures. There were three of them, and they looked like giant mechanical scorpions as tall as a man. One hissed and leapt at Voyd, attaching to his face. He yelled and yanked it off, bringing a sizable portion of his skin with the creature.

He yelled in pain and warning, collapsing to the ground. The three machines quickly swarmed onto him.

Lynx and Trinity heard Voyd's yell. They looked at each other, and Lynx grabbed a flashlight. Trinity ran to the Core and picked out a plasma gun. On their way back, they met Phoenix.

"You heard it too?" Trinity asked. He nodded. They continued down the passageway, Lynx shining the flashlight around them. The light fell on a form.

"Oh, God," Lynx said, dropping the light and sinking to the floor, hands over her mouth. Three machines huddled around Voyd, picking at his face. Voyd's body was a patchwork of scratches, slashes, and deep holes. Trinity fired at the exact same moment as Phoenix. One of the machines exploded and fell. The other two fled down the tunnel.

Lynx vomited. Phoenix grabbed her and pulled her up, leading her down the hallway. Trinity keyed her radio and rang the Core.

"Morpheus…Voyd's been killed. There's some sort of machines loose in the ship. I have to get it before it causes damage. Can you track them?"

"Yes. Go straight."

Trinity dashed down the corridor, plasma gun at the ready. She came to a split in the paths. One way led towards the Core and the other path led back to the engines.

_Shit…_

"It went to the engines," Morpheus said. Trinity jogged in that direction, something about Morpheus's statement nagging at her, some sixth sense telling her something wasn't right.

"Shit! It's right behind you!"

Trinity turned around and fired. The plasma gun hit the machine on the shoulder before it tackled her. The gun skidded across the floor, clattering until it came to a stop against the wall a few feet away.

The machine put its mouth next to Trinity's face and hissed, showing long, sharp teeth. Trinity swore and hit it, doing nothing. The machine suddenly seized up, sparking and jerking, before it collapsed to the floor in a smoking heap.

Standing beyond the downed creature was Neo, holding an outstretched hand, with a look of intense concentration on his face. He helped Trinity up.

"How'd you do that?" she asked.

"I don't know," Neo answered. Trinity bent and picked up the plasma gun, continuing down towards the engine room.

She pushed the door open and looked inside cautiously. She walked to the center of the room, sweeping the area with her gun.

"All clear," she reported. Neo entered behind her, looking around.

"Trinity, I have a bad feeling – " he began. The final machine leapt at him from the ceiling, knocking him over to the floor. Trinity fired her weapon, knocking it backwards and into the wall. Trinity helped Neo to his feet.

A squawk came over the radio.

"Neo, what exactly did you do to the virus?"

"I severed its connection to the Source…why?"

"It's gotten a hell of a lot worse, Neo."


	13. Edge of the Precipice

**Chapter Two: Edge of the Precipice**

Neo stood on the roof of the building, watching the code of the Matrix through his tinted glasses. The section of the code that was the virus was an angry, glowing red, striking out and hitting humans it passed on the street. Neo sighed, his breath showing in the cold night air.

The door behind him opened and Trinity walked up to stand beside him.

"You couldn't have foreseen it," she told him. He nodded slightly, drawing her closer to him.

"I know. But that doesn't mean I couldn't have avoided it."

Trinity pushed him away to arm's length.

"Now that's stupid, something I've never expected of you," she said. "No one _but _you could have even gotten us _this _ far. So you made on mistake – you're human. That's something we can never forget if we're going to win this war."

Neo smiled slightly. "Thank you," he whispered, pulling her close again.

"I didn't do anything," she said. "Just straightened you out a little."

"I knew I kept you around for some reason."

Trinity smiled. "At least two." She brought him into a kiss.

Locke sat in the little room glaring at the hologram on the screen. It showed the machine army digging down towards Zion. They had resumed digging as soon as the virus started attacking the humans inside the Matrix. They had just passed the first section of relay cameras Locke's forces had set up.

One of the displays was filled with a Sentinel, then it flickered and died. The other camera views disappeared quickly after that, leaving the room in total blackness.

"We need to stop them he said aloud. The lights hummed back to life, revealing Locke's lieutenant and Captain Feral of the _ Nightslash._

"I have thought of a plan," Feral said.

The train pulled to a stop with the door directly in front of Neo. He entered the car, the exiting passengers giving him a wide berth. He found a seat near the back and sat down, keeping his eyes on the door. Trinity sat down next to him, watching the opposite side of the car.

Through the window to the next compartment, Neo saw an old, raggedy man. He had wild, shaggy hair and slightly wild eyes. He formed his hand into a gun and pointed it at Neo, mouthing words.

"Bang, bang. You're dead." He smiled.

Neo blinked slowly. The man was gone. Neo mentally shrugged and looked to the left again. The train started out of the station, picking up speed.

Lynx hated waiting.

It wasn't that she was impatient or overly nervous, but nothing good could happen while you were waiting. Everyone was on edge, and not everyone got along. Trouble during action was something else – that Lynx could handle. Easier just to shoot things. 

Ghost and Phoenix were _not _getting along. Lynx broke into their conversation.

"Shut up."

They both looked at her.

"You two are acting like children – worse actually. Children know when to stop fighting. God, just get along before I separate the two of you."

Ghost grew quiet and introspective. Phoenix stared at Lynx, clenching and unclenching his fists. Myst whispered something in his ear, and he visibly relaxed.

Lynx smiled. One crisis averted. She answered her cell phone.

"Lynx, go."

"Lynx, this is Fallen Angel. I've got a visual."

Lynx walked to the window and saw Neo and Trinity emerge from the subway station and walk into the Oracle's building across the street. She sighed in relief.

"Stand down, everyone," she ordered. 

Moments after entering the building, the images of Trinity and Neo faded away, revealing the program Firewall.

He smirked slightly, a human gesture. So much for rebel intelligence and unpredictability. He peered out the window as Lynx left the building, walking towards the hard line.

Predictable, once again.

He waited until Lynx and the other rebels had gathered around the phone. It rang, and Lynx reached for it. Firewall pressed a button.

The phone, and all the ground within ten feet, exploded.

The subway car suddenly screeched to a halt, dying. The lights went out. People began talking excitedly, and one woman screamed. Neo glanced left and saw a flicker in the code.

"Get down," he yelled, knocking Trinity aside. The air filled with gunfire. Neo held his hand out, slowing the bullets to a stop. A grenade clattered in through the broken window.

"Shit."

It exploded. Neo reached out with his sixth sense and pulled the explosion into himself, channeling it into his first shot. He fired out towards where he had seen a shooter, and the bullet hit the wall and exploded.

Trinity drew her weapon and stood up, firing out the window. Neo heard another explosion and the car buckled inward, giving way. Three Agents poured through the cracks.

"Trinity, run," he ordered. She nodded and leapt onto the top of the subway train, running back towards the station.

Lynx was knocked backwards into Phoenix. Then they were both thrown upwards. Myst was pushed into the building by the force of the explosion, and Fallen Angel tumbled backwards. Ghost was thrown into the air, but he twisted around and landed on his feet.

Firewall materialized in a nearby doorway. He walked towards the group of rebels, laughing slowly.

"Where is Trinity?" he asked, lifting Lynx from the ground and jamming a gun into her ear. "And where is Morpheus?"

"Morpheus is on the ship," Ghost said, slowly loosening his pistol. Firewall laughed and faded, appearing behind Ghost. He grabbed the rebel's gun hand and yanked it upwards, twisting the gun out of Ghost's grip. He jabbed two fingers into Ghost's throat and the rebel collapsed.

Myst had her gun out in a flash, firing twice. Firewall moved left then back right, dodging the bullets. He appeared in front of Myst and shot his fist out, smacking her in the nose. She stumbled backwards a few steps and Firewall leapt into the air, spinning around backwards and hitting her left cheek with his foot. She fell.

Phoenix fired from two feet away. Firewall ducked under the bullet and rose back up, hitting Phoenix under the chin with a fist. Phoenix gasped, hands flying to his throat. The program hit him in the stomach, making him bend over, and then pushed him to the ground.

Fallen Angel was next. Firewall attacked from the front, and Fallen Angel blocked the first two attacks. The program swept a foot inwards and brought it shooting back, tripping Fallen Angel. The rebel leapt into the air, coming down on his feet. Firewall jumped straight up, kicking out and connecting with Fallen Angel's head. Fallen Angel flipped over backwards, landing on his feet. Firewall kicked out at his stomach and sent him crashing to the ground. In a flash he was on him.

"Trinity. Now," he ordered.

Trinity hit the ground behind the subway train and rolled, coming to a rest on one knee. She got to her feet and ran forward, heading for the station platform. Bullets flew through the air behind her, hitting the ground and walls. She dove for the platform and rolled onto it.

She turned around and fired twice, hitting a SWAT program in the chest. The program jerked and fell. Two SWAT opened fire, bullets cutting through the air. Trinity jumped into the air, kicking one on the head with a roundhouse kick and slamming into the other one's back. The program stumbled forward and dropped his gun.

Trinity caught the strap with her foot and flipped it into the air. It spiraled around and she caught it, reversing it and pumping a clip into the last remaining SWAT.

Neo blocked the first attack, and the second, but the third broke through. It stung for a little while, but Neo shoved the pain aside and threw the Agent out of the subway window.

The other two Agents approached from either side. Neo kicked out sideways, and the Agent caught his foot in two hands. Neo pushed off the program, striking the other Agent in the head with his foot. Neo then brought his other foot around, slamming the first Agent into the second Agent. They both collapsed.

Trinity saw Neo glide down from the sky to land three feet in front of her. She walked forward to greet him.

"What happened?"

He suddenly shot out, striking her in the shoulder. She stumbled backwards from the force of the blow. Neo's skin fell away, revealing Firewall.

"Hello, Trinity," he said. "I believe we have some unfinished business."

Fallen Angel rounded the corner to see Firewall attack Trinity. He swore and ran to join the battle. Lynx and Phoenix came around the corner next, supporting each other. Phoenix laid Lynx against a wall.

"Stay here," he said. "I'm gonna get some fire support."

Lynx's phone rang.

"Yes, Captain?"

"There's a SWAT team coming your way, Lynx," Morpheus told her. "You and Phoenix will have to hold off the team while Fallen Angel and Myst help Trinity."

Lynx nodded and hung up, climbing tiredly to her feet. Myst dashed past her, following Fallen Angel. Lynx waved at Phoenix to attract his attention and pointed down the street, mouthing the word "SWAT."

Trinity blocked a high kick and slammed a fist into Firewall's stomach. The program caught the fist and used it as a brace, flipping over Trinity's back and shoving her forward. Fallen Angel grabbed her and helped her back up. Myst joined them.

"Well, we have Trinity, Fallen Angel, and Myst," Firewall said, half to himself. "Shouldn't take too much longer then expected."

It began.

Neo walked into the Oracle's empty apartment. Glancing through the code, he saw the front door flicked and change. It opened to reveal Seraph entering through the hallway.

"Greetings," Seraph said. "You must come quickly, for there is little time."

The SWAT team proceeded down the street slowly. From behind them, they heard footsteps. Turning around almost as one, they spotted a lone girl, dressed in leather and sunglasses, come walking towards them.

"Freeze!" one yelled, pointing a rifle at her. She kept walking.

The commander thought back to the briefing. This was "Lynx," one of the terrorists on the top twenty most wanted list, along with Neo, Morpheus, and Trinity, the latter whom the SWAT had been sent to capture.

He smiled. Two would be even better. He opened a mouth to give the order to fire, and Phoenix's first shot hit him in the side of his head.

Firewall jumped into the air in front of all of them. He kicked Trinity in the head and sent her stumbling backwards. Quickly turning, he smacked Myst with the back of his foot and knocked her into Fallen Angel. He landed and dashed forward at them.

Fallen Angel slid down, hitting Firewall in the knee. The program flipped forward, hitting Fallen Angel's stomach with one hand and flipping over him. He landed in front of Myst and hit her hard in the stomach, sending her flying back. Trinity was up again and charging, but Firewall flipped over backwards, avoiding her. Fallen Angel tackled the program and brought him crashing to the floor.

Neo entered a small, busy restaurant and took a seat across from the Oracle.

"Well, it's been to long, Neo…"

He nodded.

"What went wrong? I got to the Source, but nothing happened."

"You did not get to the Source, Neo. You got to the Architect. The lies he told you were to keep you from entering the Source. He was the last line of defense, and he stopped you with only words."

Neo sighed.

"I thought it might be something like that. But it's too late to change the past. The real reason I came here was to ask – "

"What to do now."

"Yes. What do I do about this virus?"

"Now, Neo, you know that's not how it works. I can't tell you what to do, only you can do that. I am here to help you understand your choices, nothing more. You just have to make up your own damn mind."

Neo sighed again. She was always like this.

"Last time we talked, you told me we were at a crossroads, and that one path was dark and one was darker still, but had light at the end of the tunnel. Which one did we take?"

"You took the darkest path, Neo. There will be much pain between here and the end of that path, but you can make it there. Who will make it with you is a different matter entirely…"

"Trinity?"

"I cannot tell you that, Neo. I can only tell you that Trinity has seen far, and she accepts what her role will be."

The eleven remaining ships of the Zion fleet slipped into position a mile along the Sentinel's digging path. It was a desperate plan.

Feral growled. "Is the EMP fully charged?"

"Yes, Captain," said the rebel Falcon. He hefted is plasma gun and took up a position outside the ship.

"Everyone to battle stations," Feral ordered. His crew scurried about, checking the EMP and charging their plasma guns.

"Remember the plan – lasers and plasma guns first, EMPs as a last result."

Ballard's image appeared on the screen. Locke had put him in command of the entire operation.

"Tighten it up people. Twenty minutes."

Lynx stunned the first one with a shot to the throat, yanking his gun from his hand and throwing it to the next one. He jumped back in surprise, and Lynx kicked him in the chest, sending him flying backwards. She whirled around, throwing a dagger into another SWAT. A shot rang out, and one dropped to the ground, a bullet hole in the head.

Lynx smiled and motioned to the remaining SWAT. _Bring it on._

Firewall kicked Fallen Angel off him and rose, hitting the man on the head. Myst jumped on Firewall's back, yanking her dagger from her boot and stabbing him in the shoulder. He hissed in pain and threw her over his head.

Trinity came at him from the left. He yanked the dagger from his shoulder and threw it, hitting her in the stomach. Trinity collapsed to the ground, pulling the dagger from her stomach with a gasp. Firewall stood over her.

"Nobody gets past me," he said, grabbing her around the throat.

Seraph put his hand on her shoulder.

"It is time."

She got up and walked around the table, patting Neo on the back.

"It'll be alright, kid. See you soon."

Neo smiled. He sat there, thinking, after the Oracle had left. Then he followed suit.

Feral looked up when the alarm went off. Ballard's voice sounded over the loudspeakers. "Thirty seconds."

There was a sudden crash, and Feral turned to see the blue light of an EMP racing towards him.

"Oh, shit."


	14. Into the Vortex

**Chapter Three: Into the Vortex**

Neo walked on the curb of a street, balancing carefully. As he walked, he thought about the Matrix.

_it's all a just another system of control_

_ make up your own damn mind_

_ the problem is choice_

_ choose, and act_

Neo sighed again, watching the green code of his breath slip into the Matrix's master code. He watched as his simple breath created disturbances in the code.

_a butterfly flaps its wings and the weather in new york is different_

He smiled to himself. He remembered his childhood, a simple, happy childhood. He hadn't had many friends, but they had been good ones.

_it's all just another system of control_

_ My entire life had been faked. _

Trinity gasped for air. Fallen Angel rolled, kicking Firewall's feet out from under him. The program fell, and Myst darted forward, grabbing the dagger from the ground and raising it high.

Firewall twisted onto his back and kicked, hitting Myst's hand and sending the dagger flying up. He leapt to his feet and kicked the rebel away, turning in time to grab Fallen Angel's fist and hit him twice in the stomach. He turned to face Trinity again and caught the dagger as it fell. He smacked her on the back of the head and she fell into darkness.

_ The machines knew who I was since the beginning, and manipulated me into making the wrong choice from childhood. Now the real question is what is the truth?_

_The Architect's truth or the rebel's truth?_

_ Whose truth? Which truth?_

Everything changed.

_the problem is choice_

Ina flash of bright green, Neo's own code flickered and changed. He laughed out loud.

_It's a computer. Morpheus said I could bend rules, but hackers can break computer rules as easily as anything else. The problem _is _choice – my choice to believe I could not break those rules. But I can._

He took another step, and he was beside Trinity.

Lynx blocked a high swing and hit a SWAT in the neck, sending him backwards. She reversed and kicked at another SWAT and sent him flying away. Two more SWAT fell to Phoenix's bullets, and Lynx turned to look down the street at Trinity.

She fell. Suddenly, Neo appeared from nowhere. He grabbed Firewall and flung him into the side of a building. The program crashed through the wall and into the basement. Neo stared at the building, concentrating. It gave a great groan and collapsed, burying Firewall.

"Let's go," Lynx said.

_Feet pounded along a corridor. Neo came around the corner, running at full speed, his cloak trailing out behind him._

_ "Morpheus, where's Trinity?" he yelled into his phone._

_ "They got her."_

_ "Damn it! Where are they taking her?"_

_ "I don't know."_

_ "Call me back if they move."_

_ Neo glanced at the code and started running again. He reached for a door, but it flew open before his hand touched the knob._

_ "Mister Anderson…" Smith greeted him._

_ "Smith?" said Neo, shocked._

_ "Yes, it is me. I escaped the shutdown by hiding my central conciseness in a human's body. The poor man died, I believe, when I left him. No matter, "Ghost" would not have lived much longer anyway."_

_ "No…" said Neo._

_ "Yes," said Smith, raising his gun. He fired, hitting Neo in the shoulder._

_ "Your vaunted code manipulations won't work when the code is _gone._"_

_ Neo turned and ran. He smashed his way through a door and past a frozen security guard, Smith close on his heels. The former Agent fired, hitting a pipe near Neo's head. His phone rang._

_ "Neo, that seems to be some sort of explosive gas. Be careful."_

_ "I will, Morpheus. Any change with Trinity?"_

_ "They're moving her. She _might _still be alive."_

_ "Okay."_

_ Neo rounded another corner and ran straight into a rebel. Neo looked up and sighed in sudden understanding._

_ "You…"_

_ "Yes," the man said, squeezing the trigger –_

- Trinity woke with a gasp. Neo was kneeling next to her, alive and well.

"Trin?"

She smiled at him. "I'm fine. Let's get out of here."

The Sentinels streamed into the cavern, spotting the deactivated ships almost instantly. Feral swore and ran towards the door, diving out of his ship as three lasers hit it. He rolled onto the ground and grabbed a plasma gun, firing at one of the machines. It hit the Sentinel and destroyed it.

_One down, two hundred forty-four thousand to go._

Feral dropped the plasma gun and ran. He got to a spot behind a large rock formation and turned back around, yanking the pin from an EMP grenade and throwing it. It exploded in the midst of a group of Sentinels, destroying three of them.

Ballard appeared from around the corner, grabbing Feral and dragging him farther under the rocks.

"What the hell happened?" Feral said.

"Someone triggered an EMP!" Ballard said back. "It's a disaster out there. Two ships got away, but the rest are down."

"Shit."

"No kidding. We've got to try and hold out until the army passes. They'll come back for survivors."

There was an explosion nearby, and they both winced. A shadow moved across the hole of the small cave the hid inside. 

Feral motioned to Ballard to shut up. Ballard nodded. They sat and waited. The machine paused at the mouth of the tunnel, listening. After a few tense seconds, it gave up and left.

Ballard sighed in relief.

"Oh, shit," Feral said.

Neo opened his eyes. Morpheus helped him out of the chair.

"What happened in there? One minute you were with the Oracle, the next moment right beside the others."

"I had a realization," Neo explained. "The only reason my powers were limited in the Matrix was because I _chose _to believe they were. I was defeating myself. And if you _chose _to believe the body cannot live without the mind, then it won't. But you can be immortal inside the Matrix."

Morpheus shook his head.

"Neo, I just don't see how that would work. Maybe for you, because you're the One, but…"

"The One is just control, Morpheus. The reason I am the One is because I chose to believe I was! Trinity could be a One, Lynx could be a One, hell, _Voyd _could've been the One. All he needed – all any of them need – is a little help. Morpheus, _you _can be the One. The Oracle knew no one would believe this, so she told us all that we weren't the One. But we can be, Morpheus, if we choose to believe so."

Agent Matthews stood inside Room 303, his earpiece plugged into a terminal. His eyes opened.

"Reloaded," he said to himself. "Thank you."

"You are most welcome," came the voice of the Motherboard, sweet and deadly, like a beehive.

"What is my purpose?" Matthews asked.

"The virus I mutated has gone out of control. It is destroying the crop. We are already down by twenty percent. We _have _to stop it, or we will all die. These orders come directly from Dues Ex Machina."

"Yes, mistress," Matthews said. "What do I do?"

"Go to room 101. Use your key. Unlock it and walk to the far end. In a cabinet is the red switch that shuts down the Matrix temporarily. Pull it to freeze all non-independent coding – the humans, the virus, and most subroutines will be defended."

"Yes, mistress. And then?"

"I will purge the Matrix from the Source. Then we will reload it from here. During this time we will be most vulnerable to the Exiles and the rebels. You must be on your guard."

"Yes, mistress."

"However, the Anomaly has had a realization. He's unlocked the secrets of the Matrix. You are to stay here unless the Anomaly or the Guardian enters the Matrix. If they do, take the Guardian. Kill the Anomaly."

"Me?"

"No, the Virus will take care of him for us. We have a traitor inside the rebel's organization who will finish him for us."

"Yes, mistress."

"Remind this traitor not to kill him. We still need his code."

Matthews got up to leave.

"And Matthews?"

"Yes."

"Don't fail me again."

Matthews left the room at a brisk pace.

Falcon dived underneath the _Caduceus _as two Sentinels flashed by him. He rolled to the opposite side and dropped an EMP mine. It exploded, taking down the group of Sentinels harassing rebels on the ridge. They cheered and rose from cover, renewing their attacks.

The cavern shook from explosions. Falcon unhooked a grenade from his belt and threw it towards the digging machine, which was already far below. The grenade struck the massive thing and detonated, the digger grinding to a halt. Falcon whipped out his radio.

"Go for the diggers!" he shouted to everyone. He heard a few affirmatives, but most people were too busy fighting for their lives.

_If I can buy Zion only a little time…_

Falcon jumped off his perch and ran towards one of the two remaining diggers. He grabbed a mine, activated it, and dropped it down the hole. Before he could confirm a hit, he ran. The explosion lifted him up and threw him near the edge of the final digger.

Sentinels were coming at him. Falcon couldn't stand. He activated his last mine and rolled into the digger's hole.

Shadow crept out from his shelter and ran for the tripod the rebels had set up. She took a seat at the gun and powered up, turning to face the hordes of machines. She began firing, taking out three Sentinels in his first volley.

_Every little bit helps. If each rebel can destroy one Sentinel, Zion will be saved – albeit at massive cost. I only have but one life to give for my race._

The Sentinels came towards her. Shadow hit a button and powered the machine up full. As the Sentinels came within range, the gun exploded, a wave of EMP energy trailing out from the spot and destroying many.

Matthews slid his key into the lock and opened the door to room 101. He shut the door behind him and began walking forward, keeping his eyes straight ahead.

From the shadows came screams of pain and horror. Prisoners muttered brokenly to themselves, indulging in their own private fantasies. The head Agent walked quickly through the room until he reached the cabinet. He unlocked it and pulled it open, revealing a large, red switch.

He pulled it down.

"Neo!" Morpheus yelled.

"What?"

Neo walked over to the monitors and glanced at the Matrix coding over Morpheus's shoulder.

"What the hell is happening, Neo?"

"I don't know…looks like the Matrix is crashing!"

"Like the Architect said it would?"

"No, almost like its being shut down on purpose…"

"Maybe they're trying to get rid of that virus…"

"Maybe. I think so…I also think…"

"What?"

"This would be an excellent time to attack."

Sentinel 10-55A scanned the battlefield. 

ALL TARGETS DESTROYED

1 LIFE SIGNATURE FOUND

It coasted over the rocks, coming to hover above the dead body of Feral and another rebel. It charged its laser, but a new order stopped the Sentinel.

DO NOT DESTROY – ALLY

The Sentinel's reply shot back.

_diggers neutralized. orders?_

NEW DIGGERS ON THE WAY. 

A rebel ship appeared on the scene. It was small, smaller then normal. Members of the task force rushed for the ship, and it pulled its EMP, blanketing the area in blue light. Sentinels fell.

PAUSE ATTACK. DO NOT ATTACK ANY SHIPS FOR 6 HOURS.

The _Nebuchadnezzar _flew over the battlefield.

"What a disaster…" Trinity whispered.

Neo nodded. "Any survivors?"

"My computer is reading three life forms," Phoenix said. "There!"

The hovercraft coasted over the rocks, coming into a small depression where three rebels hovered: Ghost, Myst, and Ballard. They stood by the wreckage of the _Logos _arguing animatedly.

Fallen Angel lowered the hovercraft and opened the doors. The three rebels climbed on.

"What happened?" Morpheus asked.

"An EMP was triggered prematurely," Ballard explained. "When the machines broke through, it wasn't a battle – it was a slaughter."

"But one of the rebels took out the diggers. That should stall them," Myst said, hopefully.

"Good. We're going into the Matrix."


	15. Shutdown

**Chapter Four: Shutdown**

Neo and Trinity stood in the Matrix, looking across at the Mainframe building. Beside them stood two coppertops, frozen without the programs to move their bodies active.

Trinity leaned in close to Neo, so her mouth was close to his ear.

"Neo…I want to tell you something."

"What?"

"I had a vision the day we went to the sewer. It showed you, Neo, and a traitor inside the Matrix. The traitor…he killed you. I couldn't tell who it was, but it was definitely a man.

"Then a few hours ago, I had another vision. It ended the same way, but the beginning was different. It was you and Smith, talking, and Smith mentioned something about Ghost. Neo…"

"Yes?"

"Be careful tonight. Watch Ghost, I think he may be a pawn of Smith."

Neo suddenly remembered something the Oracle had said.

_trinity has seen far, and she accepts what her own role will be_

"Trinity, have these visions told you anything else?"

Trinity looked slightly troubled for a moment, and then:

"…No."

_"Okay," Morpheus said. "Here's what is going to happen."_

_ Neo took up the briefing._

_ "The Matrix has been shut down. All the humans and programs have been frozen in place except the Agents. This is the perfect time to strike. I will create a distraction for the Agents while the rest of you sneak in the back and get to the Mainframe. Once there, I will join you and hold off reinforcements until the Agent registry files can be deleted. Then, if we have enough time, we can mess with the Sentinel programming and get the hell out of there. Any questions?"_

_ "Who's operating?"_

_ "Morpheus."_

_ Lynx nodded in satisfaction. Myst spoke up._

_ "When you say "the rest of you," you mean…"_

_ "You, Trinity, Fallen Angel, and Ballard. Phoenix, Lynx, and Ghost will be on a different assignment, one involving the Merovingian."_

Neo walked straight up to the Mainframe building and knocked on the front door. The camera covering the street moved to zoom in on his face.

"Hello, Matthews," Neo said. "I know you are in there. I simply want to talk about Zion."

The intercom beeped.

"I will be right out," the Agent replied.

Trinity walked in the shadows of the alley, sneaking up on the back of the Mainframe building. She could almost _sense _ the fist approaching from behind, and she whirled around in time to block the blow.

Agent Greer stood behind her. Trinity flipped backwards, landing in a fighting stance. She motioned to him with your hand. Greer smirked arrogantly. He never saw the attack coming.

Myst's foot darted in from the right and swept the Agent off his feet. She grabbed the Agent and threw him into the wall of the building. Ballard and Fallen Angel dropped down behind him and held him to the wall. Trinity approached the subdued Agent, taking a knife out of her pocket. Greer looked at the knife in the code and started struggling against the rebel's grip.

Trinity moved forward and jabbed a gleaming knife into his stomach. Lines of silver radiated from the weapon. The Agent screamed as his body collapsed into pure light, a look of fear in his eyes as it finished him off.

"Looks like it works," Trinity observed.

"That it does," said Ballard.

"This is the place," Lynx said. Ghost nodded. Phoenix dropped down from the first floor window and started walking towards the nightclub. Lynx rolled her eyes and dropped into a crouch, running to the side and flanking the guards.

Phoenix walked up to the door.

"You!" said one of the guards. "Drake told us to watch out for you."

"I just want to talk to the Merovingian," Phoenix said.

"After the trouble you caused at the Chateau? I don't think so."

The guard drew a gun and pointed it at Phoenix's head.

"So be it," said Phoenix. He grabbed the guard's wrist and twisted it, turning the gun around and firing into him. Lynx got the drop on another guard from the shadows, hitting him in the head twice. Ghost grabbed the third guard from behind and broke his neck.

"Let's go," Lynx said, leading them into the club.

The Trainman walked out of the subway car and stood in his station, looking around. He heard footsteps approaching. The Trainman turned to face the man. 

"Smith!"

"Me, me, me," the former Agent said, jamming his hand into the Trainman's stomach. The duplication program spread out over the Trainman's body, quickly turning him into a clone of Smith.

"We need to talk," said Lynx, guns extended outwards. The Merovingian leaned over the railing and looked down.

"About what, exactly?" he asked in his heavily accented voice.

"The Matrix is vulnerable. Now is a time to strike. If you help us take it down, we will leave part of it up as a haven for you and your Exiles."

The Merovingian thought for a long time. The music in the club pounded in the rebels' ears, but the humans attending the club were frozen in place. Lynx was reminded of the party in Zion the night before the _Nebuchadnezzar _had left. 

"I will help you," said the Merovingian, "but I need assurance that we will not be betrayed."

Lynx nodded. Morpheus had expected this.

_give him something he won't be able to resist_

"Then keep Phoenix and Ghost here with you."

The Merovingian laughed. "I accept. Put down your weapons and we have a deal."

Phoenix stepped forward and dropped his gun on the floor. Ghost passed his to Lynx, and she palmed him a special program at the same time. The Merovingian's minions came forward and led the two rebels off.

"Now," the Merovingian said, "what is it you need?"

"I need to get a program into the Matrix," Lynx said. 

Matthews opened the door and stood in front of Neo.

"What is it you want, Mister Anderson?" the Agent asked.

"I want you to call off the attack on Zion," Neo said. 

"You know I cannot do that, Mister Anderson."

"If you don't, we'll strike now and deal irreparable damage."

"I highly doubt it." the Agent smirked. "You see, Smith took the Trainman, and now Lynx is dead. Your other group holds one of our agents, and he should be betraying them…now."

Neo swore. The Agent pressed a hand to his ear piece.

"They're ours. And now you are too, Mister Anderson. You see, if there's no code to manipulate, how will you fight?"

Neo realized his mistake. And he suddenly knew how much it would cost him.

The attack came from behind. Fallen Angel felt a searing pain from the back of his neck and dropped to the ground, stunned. Trinity's legs were swept out from under her, and she fell to the ground. Myst whirled around, blocking a fist from the attacker.

"You…" she hissed.

Ballard nodded.

"Since when?"

"About one month now."

"You pulled the EMP at the battle!"

He nodded again.

"Bastard! I lost friends because of you!"

Ballard laughed. "Interesting choice of words. Since we were all grown, aren't all of us truly bastards? Think about it in the long time you'll have while the Agents hold you."

Ballard's left leg slammed into the back of Myst's knee. She collapsed into a kneeling position. Ballard lifted his gun from his holster and slammed the butt into the back of her head. She dropped.

Trinity was back on her feet and dashing towards him. He moved sideways, bringing her fist across his body and flipping her over his leg. He knelt down and grabbed the dagger from her, jamming it into her leg.

"Stay put, like a good bitch," he said. He smacked her across the face with his gun.

"Come and get them," he said, knowing his new ear radio would transport his words to the Agents.

The Agent's code flickered and changed, and Neo ducked as Matthew's fist swung over his head. Neo rolled past the Agent and took off. With the Matrix inactive, he was no more powerful then any other rebel. The traitor Cypher's words came back to him.

_if you see an Agent, do what the rest of us do. run._

It had been good advice. Not heeding it had gotten Neo killed. He had a feeling the second time would be a lot worse.

He had to find Trinity. And he had to warn Lynx she was walking into a trap. How to be in two places at once?

He brought out his cell phone.

"Operator."

"Morpheus, it's a trap."

"I know. Ballard just betrayed them. He knocked Fallen Angel over, then took out Trinity and Myst. Then the code suddenly got heavily encrypted. I can't read it."

"Lynx is walking into a trap. Smith took over the Trainman."

"Shit. I wasn't watching her."

"Can you get to her in time?"

"She's there now."

Lynx stepped down off the final stairway and into the train station. A subway car screeched past the station without stopping, disturbing the trash. It swirled up the litter and threw it into the air.

From the other side of the platform approached a dim figure. 

"Trainman?" Lynx called. The man kept moving, neither slowing nor speeding up in his approach. Lynx could make out a suit, glasses…

"Shit."

Lynx turned around and ran up the stairs. Another Smith emerged from a telephone booth, lifting his gun and firing twice. Lynx winced as the bullets flew past her hair.

"Shit."

The bullets moved fast, too fast. Something was wrong. Lynx jumped around a corner, barely making it one foot off the ground.

"I am so fucked," she said to herself.

Fallen Angel rolled over and sat up. He spotted Trinity and Myst on the ground.

"Shit. Ballard."

He heard footsteps approaching. He got up and hid himself in the shadows as two Agents appeared.

"Here they are."

"Wasn't there a third?"

"He must have gotten away."

"Did the informer lie?"

"Maybe. Maybe he just failed to incapacitate him fully."

"No matter. He is after the Anomaly now."

"Yes."

One Agent lifted Trinity, the other Myst. The two programs dragged the rebels back towards the Mainframe building.

"Shit," said Fallen Angel, which was rapidly becoming the night's catchphrase. He turned and started after the Agents.

_Wait. What the hell am I doing? I can't beat _two, _especially with the Matrix deactivated. But I can stop Ballard._

He turned and started off after Ballard at a dead run.

The Merovingian entered Phoenix's and Ghost's cell. They both stood.

"Bad news for you," he said. "That…virus Smith got my Trainman. Lynx has disappeared. The deal is off."

"So…we can go?" Phoenix asked. The Merovingian laughed.

"I think not."

Ghost swore and dropped the program Lynx had palmed him earlier. It opened a hole into the street outside the club, but it could only be used once. Ghost motioned, and Phoenix jumped through, the hole closing behind him.

The Merovingian laughed again.

"So brave, to sacrifice your escape route from the man who ruined your ship."

"What do you know about that?" Ghost asked. The Merovingian raised an eyebrow.

"Haven't you guessed yet?" he asked, his hair lengthening. He pulled a pair of glasses from a pocket and put them on.

"Drake…" Ghost said in shock.

"Yes," the Merovingian said. "And now I can finish what I started…exterminating the _Logos._"

He snapped his fingers and the Twins appeared through the wall.

"Get Phoenix. I want the _Logos _crew dead. After he's gone, get to the Mainframe building and kill Myst. I will deal with Ghost."

The Twins nodded and left.

Phoenix hit the ground and started running. He got to the top of a large building and answered his ringing phone.

"Yes?"

"Phoenix, Ballard is a traitor. Can you take him out?"

"Maybe…I almost have a shot."

"Take it when you can."

"I will, sir."

Myst woke up hanging over an Agent's shoulder. The Agent carrying her opened the back door of a limo and dumped her in the back seat. Trinity was thrown on top of her.

Myst groaned. She climbed under the seat and drew her dagger from her boat. As soon as she saw one of the Agent's feet, she stabbed deep into the ankle. Then she kicked the side door open and ran off into the night.

Neo turned a corner and found himself looking into the barrel of a gun. Shifting his view, he spotted Ballard holding the gun.

"Ballard, what the fuck?"

"I'm sick of this shit, Neo. Sick of the endless fighting, sick of being cold all the time, sick of eating the same damn goop over and over again every damn day. I want this war to be over, Neo."

"Then help _us,_ Ballard, not them."

"I thought about that, Neo, and you know what I decided?"

"What?"

"I like steak more than I like bread."

Myst opened a door and almost ran straight into Seraph.

"The Oracle has been expecting you," he said. "This way."

"I have a shot," Phoenix said.

"Take it! Take it now!"

He nodded and pulled the trigger.

Fallen Angel could hear voices up ahead. He put on an extra burst of speed.

"Ballard, don't do this."

"Too late."

Phoenix pulled the trigger. A bullet rocketed from the muzzle of his sniper rifle, hurtling towards Ballard far away.

Ballard pulled the trigger. His bullet slid out of the gun. Fallen Angel saw it all as if in slow motion. He dove forward, pushing Neo out of the way. He felt the bullet pass right through him and cried out, collapsing to the ground.

Phoenix's shot hit Ballard in the head. The traitor fell to the floor.

Neo knelt down beside Fallen Angel.

"Can you hear me?"

Fallen Angel looked up. "Is he dead?"

"Yes. Thank you."

"No problem, Neo."

Neo tried to lift Fallen Angel, but the rebel cried out and fell back down.

"I'm not going to make it."

"Don't say that."

"Neo…"

"What?"

"Shut up. I'm dying. Just promise to do one thing for me."

"Anything."

"Win this damn war."

And Fallen Angel's eyes closed forever.

Lynx opened a door and ran up a staircase, quickly reaching the roof. She turned around in time to see three Smiths approaching.

"Shit."

"What happened, Morpheus? Morpheus?"

There was no answer. Phoenix shrugged and hung up the phone. He heard a shifting sound from behind him and turned around.

The Twins had returned.

"Shit."

Neo heard footsteps. He looked up.

"Greetings once again, Mister Anderson."

Myst walked into the restaurant and took a seat across from the Oracle. She nodded in greeting.

"Come closer, Myst, because I have a lot to explain."

The Oracle puffed on her cigarette and exhaled. The smoke rose from her mouth into the ceiling, where it mingled with the air there in a chaotic, unplanned mix of coding.


	16. Reload

**Chapter Five: Reload**

Myst shifted impatiently in the uncomfortable seat. A waiter came by and dropped off three drinks: a glass of soda water for the Oracle, a cup of wine for Seraph, and a Coke for Myst.

Myst smiled. It had been her favorite drink in the Matrix.

"What's happening?" she asked the Oracle after taking a sip.

"The end of this war is drawing ever closer," the Oracle said. "Neo is the only hope for mankind. He had a revelation recently, one the Architect had been using all his powers to prevent. Neo _is _the Matrix now, and there are only three people who can stop him from taking it down."

Neo stood up.

"Smith."

The former Agent nodded.

"This is the end, Mister Anderson. This is the final battle."

"I know."

"Are you prepared to die?"

"I am prepared to win, Smith."

"Then let us begin."

Phoenix fired twice. The Twins phased and Phoenix took off. He jumped onto the railing of a fire escape and slid over to the roof of the next building. One jumped over after him. Two smiled and faded down through the roof.

One took out his switchblade and flipped it open. He slashed horizontally at Phoenix, who jumped backwards and slapped the attack away. Two rose up through the ceiling and charged forward, knocking Phoenix off balance. The rebel staggered sideways and fell off the roof.

Two Agents carried Trinity up to the third floor of the Mainframe building.

"Take her to room 101," Matthews ordered. "I want the access codes before our Sentinels get to Zion. You have five hours."

"A long time ago, near the beginning of this version of the Matrix, the Motherboard summoned me into her presence. She explained that a rebel named "Niobe" had been unlocked, and that her ship would cause problems for us. She gave me amnesty for anything I might do, a secret identity, and the Twins as tools to hunt you down and kill you."

The Merovingian paused to take a sip of his wine, and then continued his tale.

"The Motherboard told me that one day the captain would set in motion events that would bring about the destruction of the Matrix. Without the Matrix, we programs could not live, either, so I agreed to help her. I contacted Niobe and over many months turned her to our cause. I planned to eliminate your crew in one fell swoop that night…but some of you escaped.

"I waited a long time before contacting Niobe again, and this time I told her that it was the last time. You and Myst would have both died if the rebels had not rescued you.

"But now I have you. Myst was captured by Agents, and she will surely be killed. Once the Twins finish off Phoenix, I will have finally destroyed you all."

Lynx backed towards the edge of the roof as the three Smiths closed in on her.

"Smith…let's talk about this," she said. The Smiths ignored her and kept coming towards the rebel.

"Ah, fuck it," Lynx said, opening fire. Surprisingly, the Smiths could not move fast enough to dodge the bullets. The three clones dropped to the ground. Lynx took off running towards the street three floors down.

"Who are those three people?" Myst asked.

"The Merovingian has put a plan into motion that might stop Neo. The Motherboard is also working against him."

"That's only two. Who is the third?"

"Smith."

"Of course."

"If either of the first two people win this skirmish, it will not matter much. If Smith wins, however, I fear he will destroy both words."

"What can we do to stop him?"

"Very little. He has almost succeeded. He nears the final battle even now."

"So there's no hope?"

"There is always hope, Myst."

"It sure doesn't seem like it."

"Myst, remember when you were at your lowest point? Niobe had betrayed you, and you were left to die on the streets. You made it out, Myst. You overcame your trial of fire. The rest should be easy."

Smith swung a fist at Neo. Neo ducked under the blow and hit Smith in the stomach. The program grunted and grabbed Neo's hand, twisting it back. Neo heard a crunching sound.

"You cannot win, Mister Anderson."

"I can try."

Neo put his foot on Smith's chest and pushed, jumping into the air. Smith staggered backwards two steps. Neo hopped onto one foot and brought his other around towards Smith's head. Smith ducked under the attack and kicked Neo's leg out from under him.

Neo fell, striking his head on the pavement. He climbed to his feet, breathing hard. He tasted blood in his mouth. Then he realized the truth of Smith's words and began running again.

One walked to the edge of the roof and looked over.

"He's gone."

Two joined his Twin at the edge, scanning the ground below.

"Where's his body?"

"Behind you, boys."

The Twins whirled around to see Phoenix swinging a metal pole into One's head. The Twin staggered backwards, then fell. He hit the ground with a crunch and groaned weakly, stunned.

Phoenix drew his pistol and pointed it down at One, switching the pole to his left hand and waving it to keep Two back.

"Don't think I won't," Phoenix warned. Two smirked.

One groaned again. Two looked down for an instant. Phoenix fired a bullet and threw the pole out, running through Two as he phased. He fired over his shoulder as he ran, reaching the roof door and yanking it open.

They strapped Trinity into a chair. Greer filled a needle and jabbed it into Trinity's arm, pressing down. Her pupils dilated. Matthews knelt down in front of her, their faces two inches apart.

"Give me the access codes to the Zion mainframe."

"Go to hell."

Ghost shook his head.

"You arrogant bastard."

The Merovingian laughed.

"Maybe. But I'm a living bastard. Unlike your crew."

"Go to hell."

"So what happens next?" Myst asked.

"I can see very little," the Oracle admitted. "I see death. Whose, I don't know. I can only tell you that tonight will be a disaster for you rebels, and if every choice made is not the right one, you will all die. Sacrifices will be made, Myst."

"Oracle…"

"Yes?"

"When I first met you, you told me I would see the end. Is that still true?"

"I do not know, Myst. So much has changed."

"You're the Oracle! How can you _not know_?"

Seraph came forward and put his hand on the Oracle's shoulder.

"It is time for you to go, Myst. Give my regards to Neo, if he survives."

"_If?_"

"Goodbye, Myst."

Seraph led the rebel out of the restaurant. The Oracle sat at the table, waiting. The lights flickered and died. She heard the door open and shut, and heard footsteps coming in her direction.

"You have gone to far this time," the Architect said. The Oracle nodded.

"I know."

"Why?" 

"I want to end this war. Your way is just a cycle of deaths and rebirths. I want a release from that cycle."

"Now you're talking like one of those damned Buddhists."

"I know."

"You have to be assimilated, Oracle. Now is the time."

"I submit."

The Oracle began to break down. Her body became a semi-solid swarm of code which broke into many pieces and floated away as if scattered by the winds.

Two of these pieces made their way outside the restaurant. Seraph watched one enter him and another combine with Myst's coding. The rebel stopped and past a hand over her eyes.

"Is something wrong?"

"No…I just felt really weird there for a second. Thank you for guiding me, Seraph."

"I am coming with you."

"Why?"

"To fulfill my purpose."

Running flat out, Phoenix entered the alleyway. The Twins approached through the buildings on both sides, reverting to normal form.

"We owe you for that," One snarled.

Phoenix fired his weapon at each Twin. They phased and returned to normal, drawing their own weapons and firing. Phoenix winced as bullets whizzed past his head and struck the brick wall behind him.

One took his switchblade out and threw it. Phoenix grabbed the blade in midair and threw it back. Two phased and the blade passed harmlessly through him.

Phoenix dove for the ringing pay phone and gratefully lifted the receiver and placed it to his ear. He felt a swirling sensation and was gone.

"We are getting aggravated."

"Yes, we are."

Neo had found his way into some sort of warehouse. He yanked open a door and ran past a human mechanic, frozen in the process of inspecting some pipes. Smith appeared behind him, firing twice and striking the pipes. Gas hissed out. Neo's phone rang.

"Morpheus!"  
"What?"

"Where is Trinity?"

"They got her, Neo." 

"Damn it. Where is everyone else?"

"Phoenix got out. They have Ghost. Lynx is being chased by Smith. Myst is with Seraph."

"Seraph?"

"Yes, she saw the Oracle."

Smith appeared from around the corner. Neo ran straight into him and stopped. Smith punched Neo, sending the frail human flying into the pipes. Neo's phone slid away.

Smith drew his gun and pointed it at Neo.

"I enjoyed watching you die the first time, Mister Anderson. I am going to enjoy it so much more the second."

Matthews grabbed the switch and pulled upwards. The code around the switch gleamed bright for a second, then the wave of brightness passed and continued its outward flow.

Smiths appeared at either side of the street. Lynx swore again. They opened fire. The bullets streaked slowly passed Lynx. She dodged each one easily.

_What the hell? It works now?_

"Why, Smith?"

"Because I must."

"What will you do when I am gone?"

"I do not know. It does not matter."

"There will be no purpose, Smith. You will die."

"After fulfilling my purpose. That is why I live."

"Very well, then. Do what you were meant to do."

"It was inevitable, Mister Anderson."

Smith pulled the trigger. The bullet flew forward in slow motion, disturbing the air around it. It streaked towards Neo and slammed into his chest.


	17. Epilogue: Rebirth

**

**_"Have you ever had a dream, Neo, that you were so sure was real? What if you were unable to wake from that dream? How would you know the difference between the dream world and the real world?"_****

**Epilogue: Rebirth**

The bullet flew through the chest, shattering bones, veins, and arteries. Blood seeped through the wound and onto the floor. Neo's vision began to fade. He saw Smith standing over him, watching. Everything went black.

Neo's heart beat slower. The flow of blood stopped. Death overtook him.

"Did it succeed?" the Agent asked.

"Yes. It is done."

"What do we do know?"

"Repair and recover. Destroy the Virus. Eliminate Zion. Send someone to gather the code."

"Yes, master."

"You did a good job, Matthews. But every good thing must end."

The Agent bowed low. "Of course."

The restart of the Matrix was more a shockwave of code restoration passing out from the Mainframe building. It caught Lynx in mid battle, shocking her. It passed Ghost as he lay in the dungeons of the Chateau. It passed the spot where the Oracle had been deleted, wiping out the last fragments of her codes. It flowed through Myst, yanking the Oracle's code from her, but leaving her with a vision.

_A figure stood with his back to Myst. He raised his arms and yelled. Destruction rained around him._

_ A train sped through a station. Morpheus lay on the floor, unconscious, while a large, unkempt man laughed hysterically. _

_ She saw a hovercraft fleeing a horde of Sentinels through the tunnels of the real world. Sentinels swarmed into Zion, spreading blood and fire in their wake. Shattered APUs littered the docks._

_ A massive ship, unlike any she had ever seen, floated beneath the ruined sky of the real world. It gave an almost bestial roar and launched bombs towards a glittering city on the horizon._

_ She saw a tall building. Smith stood on it, laughing. Seraph lay on the ground beside him, dead. She saw Trinity fighting the Twins. She saw Lynx running, Smith chasing her. She saw herself – burnt and bloodied – cradling Phoenix's head. Then she saw a single strand of code descending into blackness, and the Oracle's voice filled her thoughts._

_ "Change is the only constant in life. It is a dangerous game. Meet it well, Myst."_

The wave of rebirth swept the Oracle's code into the recycling bin of the system. Ever efficient, the bin's manager recycled the code, filtering it into two lesser programs.

These programs quickly took form. One was a woman with long, white hair and green eyes. She wore a swirling white cloak and black sunglasses. The other was a man, with black hair and pitch black eyes, who wore a black suit, black undershirt, black dress pants, and a dark pair of sunglasses.

The wave of code renewal passed through the clones of Smiths, destroying the, and returning the bodies to the control of their original inhabitants. The one surviving Smith stood over Neo, laughing still.

The wave also swept up Neo's code. It gathered the fragments spread over the Matrix by his death and bonded them into one program. This program suddenly found himself standing in front of a large pair of doors. He pushed them open.

The two programs created from the Oracle's code greeted him.

"Welcome to the lands of the dead, Neo."

**

SYSTEM FAILURE

**


End file.
